Growth-regulating Factor Proteins Research Articles

Growing Conditions and Varietal Ecologies Differently Regulates the Growth-regulating-factor (GRFs) Gene Family in Rice.

Growth-regulating factors (GRFs) are crucial in rice for controlling plant growth and development. Among the rice cultivation practices, aerobic methods are water efficient but result in significant yield reduction relative to non-aerobic cultivation. Therefore, mechanistic insights into aerobic rice cultivation are important for improving the aerobic performance of rice. This study aimed to examine the evolution of GRFs in different rice species, analyse the phenotypic differences between aerobic and non-aerobic conditions in three rice varieties, and assess the expression of GRFs in these varieties under both aerobic and non-aerobic conditions. This study comprehensively examined the GRFs gene family in 11 rice species (Oryza barthii, Oryza brachyantha, Oryza glaberrima, Oryza glumipatula, Oryza sativa subsp. indica, Oryza longistaminata, Oryza meridionalis, Oryza nivara, Oryza punctata, Oryza rufipogon, Oryza sativa subsp. japonica) focusing on phylogenetic analysis. Additionally, the expression patterns of 12 GRFs were investigated in three distinct genotypes of O. sativa subsp. indica rice, under both non-aerobic and aerobic conditions. Three major phylogenetic clades were formed based on conserved motifs in the 123 GRFs proteins in eleven rice species. Further, novel motifs were identified especially in O. longistaminata indicative of the species level evolutionary differences in rice. Among the trait performance, the number of tillers was reduced by ~ 36% under aerobic conditions, but the reduction was found to be less in CR Dhan 201, an aerobic variety. Besides, three GRFs namely GRF3, GRF4, and GRF7 were found to be distinct in expression between aerobic and non-aerobic conditions. Three GRF genes namely GRF3, GRF4, and GRF7 could be associated with the aerobic adaptation in rice.

Genome-wide identification, phylogeny, and expression analysis of GRF transcription factors in pineapple (Ananas comosus).

Pineapple is the only commercially grown fruit crop in the Bromeliaceae family and has significant agricultural, industrial, economic, and ornamental value. GRF (growth-regulating factor) proteins are important transcription factors that have evolved in seed plants (embryophytes). They contain two conserved domains, QLQ (Gln, Leu, Gln) and WRC (Trp, Arg, Cys), and regulate multiple aspects of plant growth and stress response, including floral organ development, leaf growth, and hormone responses. The GRF family has been characterized in a number of plant species, but little is known about this family in pineapple and other bromeliads. We identified eight GRF transcription factor genes in pineapple, and phylogenetic analysis placed them into five subfamilies (I, III, IV, V, VI). Segmental duplication appeared to be the major contributor to expansion of the AcGRF family, and the family has undergone strong purifying selection during evolution. Relative to that of other gene families, the gene structure of the GRF family showed less conservation. Analysis of promoter cis-elements suggested that AcGRF genes are widely involved in plant growth and development. Transcriptome data and qRT-PCR results showed that, with the exception of AcGRF5, the AcGRFs were preferentially expressed in the early stage of floral organ development and AcGRF2 was strongly expressed in ovules. Gibberellin treatment significantly induced AcGRF7/8 expression, suggesting that these two genes may be involved in the molecular regulatory pathway by which gibberellin promotes pineapple fruit expansion. AcGRF proteins appear to play a role in the regulation of floral organ development and the response to gibberellin. The information reported here provides a foundation for further study of the functions of AcGRF genes and the traits they regulate.

Genome-wide analysis of growth-regulating factor genes in grape (Vitis vinifera L.): identification, characterization and their responsive expression to osmotic stress.

Identification, characterization and osmotic stress responsive expression of growth-regulating factor genes in grape. The growth and fruit production of grape vine are severely affected by adverse environmental conditions. Growth-regulating factors (GRFs) play a vital role in the regulation of plant growth, reproduction and stress tolerance. However, their biological functions in fruit vine crops are still largely unknown. In the present study, a total number of nine VvGRFs were identified in the grape genome. Phylogenetic and collinear relationship analysis revealed that they formed seven subfamilies, and have gone through three segmental duplication events. All VvGRFs were predicted to be nucleic localized and contained both the conserved QLQ and WRC domains at their N-terminals, one of the typical structural features of GRF proteins. Quantitative real-time PCR analyses demonstrated that all VvGRFs, with a predominant expression of VvGRF7, were constitutively expressed in roots, leaves and stems of grape plants, and showed responsive expression to osmotic stress. Further growth phenotypic analysis demonstrated that ectopic expression of VvGRF7 promoted the growth and sensitivity of transgenic Arabidopsis plants to osmotic stress. Our findings provide important information for the future study of VvGRF gene functions, and potential gene resources for the genetic breeding of new fruit vine varieties with improved fruit yield and stress tolerance.

Genome-Wide Identification and Structural Characterization of Growth-Regulating Factors (GRFs) in Actinida eriantha and Actinidia chinensis.

Growth-regulating factors (GRFs) encode plant-specific transcription factors that play a vital role in regulation of plant growth, development, and stress response. Although GRFs have been identified in various plants, there is no reported work available in Actinidia (commonly known as kiwifruit) so far. In the present study, we identified 22 GRF genes on A. chinensis (hereafter A. chinensis is referred to as Ac, and GRF genes in A. chinensis are referred to as AcGRF) distributed on 17 chromosomes and one contig, and 26 GRF genes in A. eriantha (hereafter A. eriantha is referred to as Ae, and GRF genes in A. eriantha are referred to as AeGRF) distributed on 21 chromosomes. Phylogenetic analysis showed that kiwifruit GRF proteins were clustered into five distinct groups. Additionally, kiwifruit GRFs showed motif composition and gene structure similarities within the same group. Synteny analysis showed that whole-genome duplication played a key role in the expansion of the GRF family in kiwifruit. The higher expression levels of kiwifruit GRFs in young tissues and under stress conditions indicated their regulatory role in kiwifruit growth and development. We observed two genes in Ae (AeGRF6.1, AeGRF6.2) and two genes in Ac (AcGRF6.1, AeGRF6.2) significantly upregulated in different RNA-seq datasets. The presence of conserved protein structures and cis-regulatory elements caused functional divergence in duplicated gene pairs. The subcellular localization indicated the presence of kiwifruit GRFs in the nucleus of the plant cell. Protein-protein interaction analysis predicted AtGIF protein orthologs for AcGRFs and AeGRFs. Taken together, we systematically analyzed the characterization of kiwifruit GRF family members for their potential role in kiwifruit development and Pseudomonas syringae pv. actinidiae (Psa.) invasion response. Further functional studies of kiwifruit GRFs in plant growth, development, and stress response will provide valuable insights for kiwifruit breeders.

Genome-wide identification and analysis of GRF (growth-regulating factor) gene family in Camila sativa through in silico approaches

ObjectiveGRFs (growth-regulating factors) are transcription factors that significantly influence plant development and stress response. In the present study, genome-wide discovery and analysisof the CsGRF family and its significant roles in Camelina sativa development was done utilizing model GRF genes of Arabidopsis thaliana that are available in the public domain databases. MethodsGene structure analysis, exon and intron structures, phylogenetic analysis, mapping of various GRF genes on the chromosome's distribution, conserved domain analysis, and synteny analysis will be systematically categorized. Investigation of cis-regulatory elements will also be carried out using various bioinformatic approaches. ResultsIn the C. sativa genome, 19 GRF gene members and 4 GRF variants were found using publicly available genomic data. The encoding regions of GRF1, GRF2, GRF2A, and GRF8 were similar and maximal, i.e., 2046 bp, which encodes 555 amino acids, followed by GRF2. C. sativa has the most GRF gene representatives, scattered throughout six chromosomes, and appears to have 3 to 4 protein-coding regions. GRF is involved in biological processes (44.7%), molecular activities (50%), and cellular functions(24.6%). The molecular weights of GRF proteins range from 29.57 to 61.57 kDa. The majority of GRF proteins have a theoretical PI between 7.0 and 9.42. All CsGRFshave preserved QLQ and WRC (Trp, Arg, Cys) domains. All C. sativa proteins have SNH and QG (Gln, Gly) domains. The motif composition and gene structure of CsGRFs from the same sub-group were similar. In the analysis of conserved domains, the motifs of CsGRF genes were highly conserved. According to synteny investigations, large-scale duplications played a significant role in expanding the CsGRF family. ConclusionsOur findings will help tounderstand the functions of the GRF family in the evolutionary and physiological aspects of C. sativa and provide a future direction for novel work to improve crop productivity. Identifying single-gene families in multiple plant species is best to enhance crop productivity, growth, and development.

Comparative in silico analysis of Eragrostis tef (Zucc.) Trotter with other species for elucidating presence of growth regulating factors (GRFs)

Eragrostis tef (Zucc.) Trotter is becoming popular in the world due to its gluten free seeds and suitability to raise under marginal environment unlike major cereals grown worldwide. Growth Regulating Factors (GRF) are class of transcription factors involved in various biological processes and abiotic stress responses. No reports are available on characterization and phylogenetic relationships of GRFs in tef and few only in other plants. In this study, 170 GRF sequences from eleven plants were used as query to BLAST, in the available databases and resulted in four distinct EtGRFs. Two highly conserved QLQ, WRC, and the rare FFD domains were identified in selected range of GRF proteins. Phylogenetic analysis from MEGA-X clustered into 7 major groups and EtGRFs shared common ancestral route with GRFs from Setaria italica var. italica (L.) P. Beauv.), Oryza sativa subsp. indica (L.) Kato, Sorghum bicolor (L.) Moench, Panicum hallii Vasey and Zea mays subsp. mexicana (Schrad.) H. H. Iltis. Promoter analysis revealed the presence of various binding units known to play ontological roles. Protein structures and association network analysis confirmed EtGRFs as interologs to structural functions of GRF genes in closely related plants. The finding contributes to the understanding of structural and functional roles of GRFs in Eragrostis tef and other cereals.

Biological roles and an evolutionary sketch of the GRF-GIF transcriptional complex in plants

GROWTH-REGULATING FACTORs (GRFs) are sequence-specific DNA-binding transcription factors that regulate various aspects of plant growth and development. GRF proteins interact with a transcription cofactor, GRF-INTERACTING FACTOR (GIF), to form a functional transcriptional complex. For its activities, the GRF-GIF duo requires the SWITCH2/SUCROSE NONFERMENTING2 chromatin remodeling complex. One of the most conspicuous roles of the duo is conferring the meristematic potential on the proliferative and formative cells during organogenesis. GRF expression is post-transcriptionally down-regulated by microRNA396 (miR396), thus constructing the GRF-GIF-miR396 module and fine-tuning the duo’s action. Since the last comprehensive review articles were published over three years ago, many studies have added further insight into its action and elucidated new biological roles. The current review highlights recent advances in our understanding of how the GRF-GIF-miR396 module regulates plant growth and development. In addition, I revise the previous view on the evolutionary origin of the GRF gene family.

GROWTH-REGULATING FACTOR and GRF-INTERACTING FACTOR Specify Meristematic Cells of Gynoecia and Anthers.

We investigated the biological roles of the Arabidopsis (Arabidopsis thaliana) GROWTH-REGULATING FACTOR (GRF) and GRF-INTERACTING FACTOR (GIF) transcriptional complex in the development of gynoecia and anthers. There are nine GRFs and three GIFs in Arabidopsis, and seven GRFs are posttranscriptionally silenced by microRNA396 (miR396). We found that overexpression of MIR396 in the gif1 gif2 double mutant background (gif1 gif2 35S:MIR396) resulted in neither ovary nor pollen. Histological and molecular marker-based analyses revealed that the mutant gynoecial primordia failed to develop carpel margin meristems and mature flowers lacked the ovary, consisting only of the stigma, style, and replum-like tissues. The mutant anther primordia were not able to form the pluripotent archesporial cells that produce pollen mother cells and microsporangia. Multiple combinations of GRF mutations also displayed the same phenotypes, indicating that the GRF-GIF duo is required for the formation of those meristematic and pluripotent cells. Most GRF proteins are localized and abundant in those cells. We also found that the weak gynoecial defects of pinoid-3 (pid-3) mutants were remarkably exacerbated by gif1 gif2 double mutations and 35S:MIR396, so that none of the gynoecia produced by gif1 gif2 pid-3 and 35S:MIR396 pid-3 developed ovaries at all. Moreover, gif1 gif2 double mutations and 35S:MIR396 also acted synergistically with 1-N-naphthylphthalamic acid in forming aberrant gynoecia. The results altogether suggest that the GRF-GIF duo regulates the meristematic and pluripotent competence of carpel margin meristems and the archesporial cell lineage and that this regulation is implemented in association with auxin action, ultimately conferring reproductive competence on Arabidopsis.

Molecular Characterization and Expression Profiling of Tomato GRF Transcription Factor Family Genes in Response to Abiotic Stresses and Phytohormones.

Growth regulating factors (GRFs) are plant-specific transcription factors that are involved in diverse biological and physiological processes, such as growth, development and stress and hormone responses. However, the roles of GRFs in vegetative and reproductive growth, development and stress responses in tomato (Solanum lycopersicum) have not been extensively explored. In this study, we characterized the 13 SlGRF genes. In silico analysis of protein motif organization, intron–exon distribution, and phylogenetic classification confirmed the presence of GRF proteins in tomato. The tissue-specific expression analysis revealed that most of the SlGRF genes were preferentially expressed in young and growing tissues such as flower buds and meristems, suggesting that SlGRFs are important during growth and development of these tissues. Some of the SlGRF genes were preferentially expressed in fruits at distinct developmental stages suggesting their involvement in fruit development and the ripening process. The strong and differential expression of different SlGRFs under NaCl, drought, heat, cold, abscisic acid (ABA), and jasmonic acid (JA) treatment, predict possible functions for these genes in stress responses in addition to their growth regulatory functions. Further, differential expression of SlGRF genes upon gibberellic acid (GA3) treatment indicates their probable function in flower development and stress responses through a gibberellic acid (GA)-mediated pathway. The results of this study provide a basis for further functional analysis and characterization of this important gene family in tomato.

Developmental processes and responses to hormonal stimuli in tea plant (Camellia sinensis) leaves are controlled by GRF and GIF gene families.

Tea plant (Camellia sinensis (L.) O. Kuntze) is an important leaf-type woody crop used for producing of non-alcoholic beverages worldwide. The GROWTH-REGULATING FACTOR (GRF) transcription factors cooperated with GRF-INTERACTING FACTOR (GIF) transcriptional coactivators positively regulate leaf development. In the present study, six GRF and two GIF genes were identified and characterized in the leaf transcriptome of C. sinensis, respectively. The alignment results showed that the feature structures of the predicted homologous GRF and GIF proteins of C. sinensis hold a high identity with Arabidopsis and rice. The presence of C. sinensis miR396 target sites suggested that these miR396 members are the potential post-transcriptional regulators of CsGRF genes. The expression profiles of CsGRF and CsGIF1 genes were higher in tender leaves and consistently downregulated during tea plant leaf development. Those results suggested that these genes may be actively involved in the early stage leaf tissue formation in tea plant. The divergence of CsGRF and CsGIF genes in response to different hormonal stimuli revealed the possible multiple functions of these genes in hormonal regulation. This study provided the potential molecular basis of the CsGRF and CsGIF family genes for future functional research on leaf development and hormonal stimuli in C. sinensis.

Identification and transcript profiles of citrus growth-regulating factor genes involved in the regulation of leaf and fruit development.

Growth-regulating factor (GRF) is an important protein in GA-mediated response, with key roles in plant growth and development. However, it is not known whether or how the GRF proteins in citrus to regulate organ size. In this study, nine citrus GRF genes (CsGRF1-9) were validated from the 'Anliu' sweet orange (AL, Citrus sinensis cv. Anliu)by PCR amplification. They all contain two conserved motifs (QLQ and WRC) and have 3-4 exons. The transcript levels of genes were detected by qRT-PCR. Transcript analysis showed that (1) CsGRF 1, 2, 5, 6, 7, and 9 expressed predominantly in young leaf, CsGRF 3 and 4 expressed predominantly in fruit immature juice sacs and CsGRF 8 expressed predominantly in root; (2) all citrus GRF genes had significantly higher expression in young leaves than mature leaf; (3) in juice sacs, the transcript levels of CsGRF1, 4, 5, 6, and 8 increased significantly while the transcript levels of CsGRF2, 3, 7, and 9 had no significant change from 80 DAF to 100 DAF. Besides, GA3 treatment did not affect the transcript levels of CsGRF5 and CsGRF6 but significantly increased the transcript levels of the other seven CsGRF genes in young leaves. These results suggested that all CsGRF genes involve in the leaf development, CsGRF1, 4, 5, 6, and 8 act developmentally whilst CsGRF2, 3, 7, and 9 play fundamental roles in fruit cell enlargement, which may be through GA pathway or GA-independent pathway.

Order-wide in silico comparative analysis and identification ofgrowth-regulating factor proteins in Malpighiales

Malpighiales, containing approximately 16,000 species, is one of the largest and most diverse angiosperm orders in plants. Growth-regulating factor (GRF) protein is a putative transcription factor and plays a regulatory role during plant growth and development processes such as stem elongation and cell expansion. The latest available protein data provide an opportunity to compare and understand the critical similarities and differentiation in GRF proteins among Malpighiales members. In the present study we conducted domain, two- and three-dimensional (2D, 3D) comparative, physicochemical, subcellular prediction, and sequence analysis of 87 putative GRF proteins belonging to 4 genera in Malpighiales using different bioinformatic tools. The results showed that QLQ, WRC, TQL, GGPL, RSRKPVE, FDV, and GFG domain motifs are conserved in rates between 34% and 82%. Comparative analysis proved that there is a common triangle-like shape among GRF proteins, and the conserved motifs are localized in similar regions of this triangle. The sequence lengths of GRFs change between 93 and 639 aa, and pH values differ between 5.28 and 10.50. According to subcellular prediction and domain analysis, only 9%-11% of GRFs are localized out of the nuclear region. Additionally, it was determined that 87 GRF proteins have monophyletic phylogeny. The average values of pairwise distance and nucleotide diversity (?) were 2.78 and 0.727, respectively. These results may contribute to an understanding of how structurally similar but functionally diverse GRF proteins execute various functions in different plant parts or in different plant species.

Genome-wide identification and analysis of the growth-regulating factor family in Chinese cabbage (Brassica rapa L. ssp. pekinensis).

BackgroundGrowth regulating factors (GRFs) have been shown to play important roles in plant growth and development. GRF genes represent a large multigene family in plants. Recently, genome-wide structural and evolutionary analyses of the GRF gene families in Arabidopsis, rice, and maize have been reported. Chinese cabbage (Brassica rapa L. ssp. pekinensis) is one of the most important vegetables for agricultural production, and a full genome assembly for this plant has recently been released. However, to our knowledge, the GRF gene family from Chinese cabbage has not been characterized in detail.ResultsIn this study, genome-wide analysis was carried out to identify all the GRF genes in Chinese cabbage. Based on the complete Chinese cabbage genome sequence, 17 nonredundant GRF genes, named BrGRFs, were identified and classified into six groups. Phylogenetic analysis of the translated GRF protein sequences from Chinese cabbage, Arabidopsis, and rice indicated that the Chinese cabbage GRF proteins were more closely related to the GRF proteins of Arabidopsis than to those of rice. Expression profile analysis showed that the BrGRF genes had uneven transcript levels in different organs or tissues, and the transcription of most BrGRF genes was induced by gibberellic acid (GA3) treatment. Additionally, over-expression of BrGRF8 in transgenic Arabidopsis plants increased the sizes of the leaves and other organs by regulation of cell proliferation.ConclusionsThe data obtained from this investigation will contribute to a better understanding of the characteristics of the GRF gene family in Chinese cabbage, and provide a basis for further studies to investigate GRF protein function during development as well as for Chinese cabbage-breeding programs to improve yield and/or head size.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-807) contains supplementary material, which is available to authorized users.

Genome-wide identification and analysis of growth regulating factor genes in Brachypodium distachyon: in silico approaches

Growth-regulating factor (GRF) genes may play important roles for regulating growth and development in different plant tissues and organs. Here we report the first genome-wide analysis of the GRF gene family in Brachypodium. We performed in silico comparative analysis of GRF genes, including their structure, duplication in the genome, conserved motifs, and phylogenetic relationship. At the end of the study, 10 BdGRF genes were identified. The highest number of GRF genes was identified on chromosome 1 with 5 members, whereas the least number of genes (only 1 member) was found on chromosomes 2, 4, and 5. Of those, a single segmental duplication was observed in the Brachypodium genome. Average exon and intron numbers were determined as 3 and 4, respectively. Motif analysis showed that WRC and QLQ residues were consistent in all GRF protein sequences. Gene Ontology terms showed that 10 BdGRF proteins grouped in the same biological function, biological process, and cellular component groups. In addition, we compared the new BdGRF proteins with the other monocot and dicot GRF proteins sequences. Phylogenetic analysis revealed that GRF proteins of monocot and dicot species were clustered together in a joined tree; in particular, the monocot species (Brachypodium, maize, and rice) were grouped into the same cluster with high bootstrap values. We assume that the results of this study will provide molecular insights about GRF proteins in grass species.

Isolation and characterization of genes encoding GRF transcription factors and GIF transcriptional coactivators in Maize ( Zea mays L.)

It has been a long-held view that regulation of gene expression in eukaryotes occurs predominantly at the transcriptional level. GRF (Growth-regulating factor) and GIF (GRF-interacting factor) proteins are putative novel transcriptional regulators and coactivators which form protein complexes and are involved in regulating the growth and development of certain tissues and/or organs in plants. In this study, 14 homologs of ZmGRF genes and 3 homologs of ZmGIF genes from maize ( Zea mays L.) were identified and characterized. Fourteen GRF proteins were divided into three subfamilies. ZmGRF genes of C subfamily were mainly expressed in immature ears. Furthermore, overexpression of both ZmGRF11– ZmGIF2 and ZmGRF2– ZmGIF3 resulted in delayed bolting but accelerating the growth of inflorescence stem when compared to wild-type Arabidopsis thaliana. As a result, we postulated that these four genes which expressed preferentially in immature ear tissues in maize might play important roles in the growth and development of ears and might contribute to improving corn yields.