scholarly journals Expansion and innovation in auxin signaling: where do we grow from here?

Development ◽  
2021 ◽  
Vol 148 (5) ◽  
pp. dev187120
Author(s):  
Román Ramos Báez ◽  
Jennifer L. Nemhauser
Keyword(s):  
Transcription Factors ◽  
Gene Families ◽  
Flowering Plants ◽  
Auxin Signaling ◽  
Regulation Of Transcription ◽  
Functional Diversification ◽  
Auxin Action ◽  
Primary Mechanism ◽  
Almost All ◽  
Developmental Responses

ABSTRACTThe phytohormone auxin plays a role in almost all growth and developmental responses. The primary mechanism of auxin action involves the regulation of transcription via a core signaling pathway comprising proteins belonging to three classes: receptors, co-receptor/co-repressors and transcription factors. Recent studies have revealed that auxin signaling can be traced back at least as far as the transition to land. Moreover, studies in flowering plants have highlighted how expansion of the gene families encoding auxin components is tied to functional diversification. As we review here, these studies paint a picture of auxin signaling evolution as a driver of innovation.

scholarly journals Auxin Response Factors — output control in auxin biology

2017 ◽  
Author(s):  
Mark Roosjen ◽  
Sébastien Paque ◽  
Dolf Weijers
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Structural Biology ◽  
Auxin Signaling ◽  
Auxin Response ◽  
Response Factors ◽  
Output Control ◽  
Auxin Response Factors ◽  
Almost All ◽  
Near Future

AbstractThe phytohormone auxin is involved in almost all developmental processes in land plants. Most, if not all, of these processes are mediated by changes in gene expression. Auxin acts on gene expression through a short nuclear pathway that converges upon the activation of a family of DNA-binding transcription factors. These AUXIN RESPONSE FACTORS (ARFs) are thus the effector of auxin response and translate the chemical signal to the regulation of a defined set of genes. Given the limited number of dedicated components in auxin signaling, distinct properties among the ARF family likely contributes to the establishment of multiple unique auxin responses in plant development. In the two decades following the identification of the first ARF in Arabidopsis much has been learnt about how these transcription factors act, and how they generate unique auxin responses. Progress in genetics, biochemistry, genomics and structural biology have helped to develop mechanistic models for ARF action. However, despite intensive efforts, many central questions are yet to be addressed. In this review we highlight what has been learnt about ARF transcription factors, and identify outstanding questions and challenges for the near future.

scholarly journals The reference genome and transcriptome of the limestone langur, Trachypithecus leucocephalus, reveal expansion of genes related to alkali tolerance

BMC Biology ◽  
2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Tengcheng Que ◽  
Huifeng Wang ◽  
Weifei Yang ◽  
Jianbao Wu ◽  
Chenyang Hou ◽  
...  
Keyword(s):  
De Novo ◽  
Great Majority ◽  
Gene Families ◽  
Functional Enrichment ◽  
Mineral Absorption ◽  
Iron Storage ◽  
Trachypithecus Leucocephalus ◽  
Karst Environment ◽  
Alkali Tolerance ◽  
Almost All

Abstract Background Trachypithecus leucocephalus, the white-headed langur, is a critically endangered primate that is endemic to the karst mountains in the southern Guangxi province of China. Studying the genomic and transcriptomic mechanisms underlying its local adaptation could help explain its persistence within a highly specialized ecological niche. Results In this study, we used PacBio sequencing and optical assembly and Hi-C analysis to create a high-quality de novo assembly of the T. leucocephalus genome. Annotation and functional enrichment revealed many genes involved in metabolism, transport, and homeostasis, and almost all of the positively selected genes were related to mineral ion binding. The transcriptomes of 12 tissues from three T. leucocephalus individuals showed that the great majority of genes involved in mineral absorption and calcium signaling were expressed, and their gene families were significantly expanded. For example, FTH1 primarily functions in iron storage and had 20 expanded copies. Conclusions These results increase our understanding of the evolution of alkali tolerance and other traits necessary for the persistence of T. leucocephalus within an ecologically unique limestone karst environment.

scholarly journals Genome-Wide Identification and Comparative Analysis for OPT Family Genes in Panax ginseng and Eleven Flowering Plants

Molecules ◽  
2018 ◽  
Vol 24 (1) ◽  
pp. 15 ◽  
Author(s):  
He Su ◽  
Yang Chu ◽  
Junqi Bai ◽  
Lu Gong ◽  
Juan Huang ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Panax Ginseng ◽  
Expression Patterns ◽  
Flowering Plants ◽  
Functional Development ◽  
Wide Range ◽  
Organ Specific ◽  
Genome Level ◽  
Negative Links ◽  
Global Platform

Herb genomics and comparative genomics provide a global platform to explore the genetics and biology of herbs at the genome level. Panax ginseng C.A. Meyer is an important medicinal plant for a variety of bioactive chemical compounds of which the biosynthesis may involve transport of a wide range of substrates mediated by oligopeptide transporters (OPT). However, information about the OPT family in the plant kingdom is still limited. Only 17 and 18 OPT genes have been characterized for Oryza sativa and Arabidopsis thaliana, respectively. Additionally, few comprehensive studies incorporating the phylogeny, gene structure, paralogs evolution, expression profiling, and co-expression network between transcription factors and OPT genes have been reported for ginseng and other species. In the present study, we performed those analyses comprehensively with both online tools and standalone tools. As a result, we identified a total of 268 non-redundant OPT genes from 12 flowering plants of which 37 were from ginseng. These OPT genes were clustered into two distinct clades in which clade-specific motif compositions were considerably conservative. The distribution of OPT paralogs was indicative of segmental duplication and subsequent structural variation. Expression patterns based on two sources of RNA-Sequence datasets suggested that some OPT genes were expressed in both an organ-specific and tissue-specific manner and might be involved in the functional development of plants. Further co-expression analysis of OPT genes and transcription factors indicated 141 positive and 11 negative links, which shows potent regulators for OPT genes. Overall, the data obtained from our study contribute to a better understanding of the complexity of the OPT gene family in ginseng and other flowering plants. This genetic resource will help improve the interpretation on mechanisms of metabolism transportation and signal transduction during plant development for Panax ginseng.

scholarly journals Novel Transcriptional Mechanisms for Regulating Metabolism by Thyroid Hormone

2018 ◽  
Vol 19 (10) ◽  
pp. 3284 ◽  
Author(s):  
Brijesh Kumar Singh ◽  
Rohit Anthony Sinha ◽  
Paul Michael Yen
Keyword(s):  
Transcription Factors ◽  
Thyroid Hormone ◽  
Target Genes ◽  
Regulation Of Transcription ◽  
Post Translational Modification ◽  
Hormone Response Elements ◽  
Conventional View ◽  
Metabolic Genes ◽  
Activation Of Transcription ◽  
Rna Transcript

The thyroid hormone plays a key role in energy and nutrient metabolisms in many tissues and regulates the transcription of key genes in metabolic pathways. It has long been believed that thyroid hormones (THs) exerted their effects primarily by binding to nuclear TH receptors (THRs) that are associated with conserved thyroid hormone response elements (TREs) located on the promoters of target genes. However, recent transcriptome and ChIP-Seq studies have challenged this conventional view as discordance was observed between TH-responsive genes and THR binding to DNA. While THR association with other transcription factors bound to DNA, TH activation of THRs to mediate effects that do not involve DNA-binding, or TH binding to proteins other than THRs have been invoked as potential mechanisms to explain this discrepancy, it appears that additional novel mechanisms may enable TH to regulate the mRNA expression. These include activation of transcription factors by SIRT1 via metabolic actions by TH, the post-translational modification of THR, the THR co-regulation of transcription with other nuclear receptors and transcription factors, and the microRNA (miR) control of RNA transcript expression to encode proteins involved in the cellular metabolism. Together, these novel mechanisms enlarge and diversify the panoply of metabolic genes that can be regulated by TH.

scholarly journals Expression and Regulation of Transcription Factors GATA-4 and GATA-6 in Developing Mouse Testis1

Endocrinology ◽  
1999 ◽  
Vol 140 (3) ◽  
pp. 1470-1480 ◽  
Author(s):  
Ilkka Ketola ◽  
Nafis Rahman ◽  
Jorma Toppari ◽  
Malgorzata Bielinska ◽  
Susan B. Porter-Tinge ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Regulation Of Transcription

scholarly journals Genome-Wide Identification and Analysis of the WRKY Gene Family and Cold Stress Response in Acer truncatum

Genes ◽  
2021 ◽  
Vol 12 (12) ◽  
pp. 1867
Author(s):  
Yan Li ◽  
Xiang Li ◽  
Jiatong Wei ◽  
Kewei Cai ◽  
Hongzhi Zhang ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Stress Response ◽  
Cold Stress ◽  
Gene Family ◽  
Gene Families ◽  
Regulatory Function ◽  
Wrky Gene ◽  
Wrky Transcription Factors ◽  
Biotic Stresses ◽  
Genome Wide

WRKY transcription factors constitute one of the largest gene families in plants and are involved in many biological processes, including growth and development, physiological metabolism, and the stress response. In earlier studies, the WRKY gene family of proteins has been extensively studied and analyzed in many plant species. However, information on WRKY transcription factors in Acer truncatum has not been reported. In this study, we conducted genome-wide identification and analysis of the WRKY gene family in A. truncatum, 54 WRKY genes were unevenly located on all 13 chromosomes of A. truncatum, the highest number was found in chromosomes 5. Phylogenetic relationships, gene structure, and conserved motif identification were constructed, and the results affirmed 54 AtruWRKY genes were divided into nine subgroup groups. Tissue species analysis of AtruWRKY genes revealed which were differently exhibited upregulation in flower, leaf, root, seed and stem, and the upregulation number were 23, 14, 34, 18, and 8, respectively. In addition, the WRKY genes expression in leaf under cold stress showed that more genes were significantly expressed under 0, 6 and 12 h cold stress. The results of this study provide a new insight the regulatory function of WRKY genes under abiotic and biotic stresses.

scholarly journals Transcriptional Regulation of Hydrogen Peroxide and Calcium for Signaling Transduction and Stress-defensive Genes Contributing to Improved Drought Tolerance in Creeping Bentgrass

2020 ◽  
Vol 145 (4) ◽  
pp. 236-246
Author(s):  
Zhou Li ◽  
Yan Peng ◽  
Bingru Huang
Keyword(s):  
Transcription Factors ◽  
Drought Stress ◽  
Drought Tolerance ◽  
Creeping Bentgrass ◽  
Grass Species ◽  
Regulation Of Transcription ◽  
Signaling Transduction ◽  
Genes Expression ◽  
Protective Genes ◽  
Ca Signaling

Small molecules, including H2O2 and Ca, mediate stress signaling and drought tolerance in plants. The objective of this study was to determine whether improvement in drought tolerance by H2O2 and Ca were associated with the regulation of transcription factors and stress-protective genes in perennial grass species. Plants of creeping bentgrass (Agrostis stolonifera) were sprayed with water (control), H2O2 (9 mm), or CaCl2 (10 mm) and exposed to drought stress for 20 days in controlled-environment growth chambers. Foliar application of H2O2 or Ca led to significant improvement in drought tolerance of creeping bentgrass, as demonstrated by greater turf quality, leaf relative water content, chlorophyll content, photochemical efficiency, and cell membrane stability, as compared with the untreated control. The application of H2O2 and Ca resulted in significant up-regulation of genes in Ca signaling transduction pathways [Ca-dependent kinase 26 (CDPK26), mitogen-activated protein kinase 1 (MAPK1), and 14-3-3] and transcript factors (WRKY75 and MYB13). For genes encoding antioxidant enzymes, H2O2 mainly enhanced superoxide dismutase (SOD), catalase (CAT), glutathione reductase (GR), and dehydroascorbate reductase (DHAR) expression, while Ca primarily improved transcript levels of SOD, monodehydroascorbate reductase (MDHAR), and GR. In addition, heat shock protein 70 (HSP70), metallothionein 1 (MT1), and glutamine synthetase 2 (GS2) were also markedly up-regulated by H2O2 and Ca under drought stress. However, the transcript level of lipoxygenase 3 (LOX3) was significantly down-regulated by H2O2 and Ca under well-watered and drought conditions. These results imply that H2O2 and Ca commonly or differentially regulate genes expression in association with drought tolerance through activating Ca signaling pathway and regulating transcription factors and stress-protective genes expression, leading to the alleviation of lipid peroxidation, maintenance of correct protein folding and translocation, and enhancement of nitrogen metabolism under a prolonged period of drought stress in creeping bentgrass.

scholarly journals Transcription Factors and microRNA Genes Regulatory Network Construction Under Drought Stress in Sesame (Sesamum indicum L.)

2020 ◽  
Author(s):  
Mohammad Amin Baghery ◽  
Seyed Kamal Kazemitabar ◽  
Ali Dehestani ◽  
Pooyan Mehrabanjoubani ◽  
Mohammad Mehdi Naghizadeh ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Drought Stress ◽  
Gene Networks ◽  
Regulatory Networks ◽  
Regulatory Gene ◽  
Sesamum Indicum ◽  
Regulatory Mechanisms ◽  
Oilseed Crop ◽  
Sesame Genotypes ◽  
Almost All

Abstract Background: Drought is one of the most common environmental stresses affecting crops yield and quality. Sesame is an important oilseed crop that most likely faces drought during its growth due to growing in semi-arid and arid areas. Plants responses to drought controlled by regulatory mechanisms. Despite this importance, there is little information about Sesame regulatory mechanisms against drought stress. Results: 458 drought-related genes were identified using comprehensive RNA-seq data analysis of two susceptible and tolerant sesame genotypes under drought stress. These drought-responsive genes were included secondary metabolites biosynthesis-related Like F3H, sucrose biosynthesis-related like SUS2, transporters like SUC2, and protectives like LEA and HSP families. Interactions between identified genes and regulators including TFs and miRNAs were predicted using bioinformatics tools and related regulatory gene networks were constructed. Key regulators and relations of Sesame under drought stress were detected by network analysis. TFs belonged to DREB (DREB2D), MYB (MYB63), ZFP (TFIIIA), bZIP (bZIP16), bHLH (PIF1), WRKY (WRKY30) and NAC (NAC29) families were found among key regulators. mRNAs like miR399, miR169, miR156, miR5685, miR529, miR395, miR396, and miR172 also found as key drought regulators. Furthermore, a total of 117 TFs and 133 miRNAs that might be involved in drought stress were identified with this approach. Conclusions: Most of the identified TFs and almost all of the miRNAs are introduced for the first time as potential regulators of drought response in Sesame. These regulators accompany with identified drought-related genes could be valuable candidates for future studies and breeding programs on Sesame under drought stress. Keywords: Sesamum indicum, Drought stress, Regulatory networks, miRNA, Transcription Factors.

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