scholarly journals Transcriptome-Wide Identification, Evolutionary Analysis, and GA Stress Response of the GRAS Gene Family in Panax ginseng C. A. Meyer

Plants ◽  
2020 ◽  
Vol 9 (2) ◽  
pp. 190
Author(s):  
Nan Wang ◽  
Kangyu Wang ◽  
Shaokun Li ◽  
Yang Jiang ◽  
Li Li ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Stress Response ◽  
Panax Ginseng ◽  
Perennial Herb ◽  
Evolutionary Analysis ◽  
Physiological Processes ◽  
Variation Function ◽  
Plant Signal Transduction ◽  
Gras Gene

GRAS transcription factors are a kind of plant-specific transcription factor that have been found in a variety of plants. According to previous studies, GRAS proteins are widely involved in the physiological processes of plant signal transduction, stress, growth and development. The Jilin ginseng (Panax ginseng C.A. Meyer) is a heterogeneous tetraploid perennial herb of the Araliaceae family, ginseng genus. Important information regarding the GRAS transcription factors has not been reported in ginseng. In this study, 59 Panax ginseng GRAS (PgGRAS) genes were obtained from the Jilin ginseng transcriptome data and divided into 13 sub-families according to the classification of Arabidopsis thaliana. Through systematic evolution, structural variation, function and gene expression analysis, we further reveal GRAS’s potential function in plant growth processes and its stress response. The expression of PgGRAS genes responding to gibberellin acids (GAs) suggests that these genes could be activated after application concentration of GA. The qPCR analysis result shows that four PgGRAS genes belonging to the DELLA sub-family potentially have important roles in the GA stress response of ginseng hairy roots. This study provides not only a preliminary exploration of the potential functions of the GRAS genes in ginseng, but also valuable data for further exploration of the candidate PgGRAS genes of GA signaling in Jilin ginseng, especially their roles in ginseng hairy root development and GA stress response.

scholarly journals The impact of bZIP Atf1ortholog global regulators in fungi

2021 ◽  
Author(s):  
Éva Leiter ◽  
Tamás Emri ◽  
Klaudia Pákozdi ◽  
László Hornok ◽  
István Pócsi
Keyword(s):  
Transcription Factors ◽  
Stress Response ◽  
Secondary Metabolite ◽  
Plant Pathogens ◽  
Leucine Zipper ◽  
Secondary Metabolite Production ◽  
Special Focus ◽  
Human Pathogens ◽  
Metabolite Production ◽  
The Impact

Abstract Regulation of signal transduction pathways is crucial for the maintenance of cellular homeostasis and organismal development in fungi. Transcription factors are key elements of this regulatory network. The basic-region leucine zipper (bZIP) domain of the bZIP-type transcription factors is responsible for DNA binding while their leucine zipper structural motifs are suitable for dimerization with each other facilitiating the formation of homodimeric or heterodimeric bZIP proteins. This review highlights recent knowledge on the function of fungal orthologs of the Schizosaccharomyces pombe Atf1, Aspergillus nidulans AtfA, and Fusarium verticillioides FvAtfA, bZIP-type transcription factors with a special focus on pathogenic species. We demonstrate that fungal Atf1-AtfA-FvAtfA orthologs play an important role in vegetative growth, sexual and asexual development, stress response, secondary metabolite production, and virulence both in human pathogens, including Aspergillus fumigatus, Mucor circinelloides, Penicillium marneffei, and Cryptococcus neoformans and plant pathogens, like Fusarium ssp., Magnaporthe oryzae, Claviceps purpurea, Botrytis cinerea, and Verticillium dahliae. Key points • Atf1 orthologs play crucial role in the growth and development of fungi. • Atf1 orthologs orchestrate environmental stress response of fungi. • Secondary metabolite production and virulence are coordinated by Atf1 orthologs.

Clade III cytokinin response factors share common roles in response to oxidative stress responses linked to cytokinin synthesis

2021 ◽  
Vol 72 (8) ◽  
pp. 3294-3306
Author(s):  
Ariel M Hughes ◽  
H Tucker Hallmark ◽  
Lenka Plačková ◽  
Ondrej Novák ◽  
Aaron M Rashotte
Keyword(s):  
Oxidative Stress ◽  
Transcription Factors ◽  
Stress Response ◽  
Stress Responses ◽  
Oxidative Stress Response ◽  
Response Factors ◽  
Ontology Term ◽  
Regulated Expression ◽  
Cytokinin Response ◽  
Oxidative Stress Responses

Abstract Cytokinin response factors (CRFs) are transcription factors that are involved in cytokinin (CK) response, as well as being linked to abiotic stress tolerance. In particular, oxidative stress responses are activated by Clade III CRF members, such as AtCRF6. Here we explored the relationships between Clade III CRFs and oxidative stress. Transcriptomic responses to oxidative stress were determined in two Clade III transcription factors, Arabidopsis AtCRF5 and tomato SlCRF5. AtCRF5 was required for regulated expression of >240 genes that are involved in oxidative stress response. Similarly, SlCRF5 was involved in the regulated expression of nearly 420 oxidative stress response genes. Similarities in gene regulation by these Clade III members in response to oxidative stress were observed between Arabidopsis and tomato, as indicated by Gene Ontology term enrichment. CK levels were also changed in response to oxidative stress in both species. These changes were regulated by Clade III CRFs. Taken together, these findings suggest that Clade III CRFs play a role in oxidative stress response as well as having roles in CK signaling.

Classification of hepatitis C virus into major types and subtypes based on molecular evolutionary analysis

1995 ◽  
Vol 36 (2-3) ◽  
pp. 201-214 ◽  
Author(s):  
Ken-ichi Ohba ◽  
Masashi Mizokami ◽  
Tomoyoshi Ohno ◽  
Kaoru Suzuki ◽  
Etsuro Orito ◽  
...  
Keyword(s):  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Evolutionary Analysis ◽  
Molecular Evolutionary Analysis

scholarly journals Increasing Oxygen Partial Pressures Induce a Distinct Transcriptional Response in Human PBMC: A Pilot Study on the “Normobaric Oxygen Paradox”

2021 ◽  
Vol 22 (1) ◽  
pp. 458
Author(s):  
Deborah Fratantonio ◽  
Fabio Virgili ◽  
Alessandro Zucchi ◽  
Kate Lambrechts ◽  
Tiziana Latronico ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Transcription Factors ◽  
Stress Response ◽  
Mononuclear Cells ◽  
Human Peripheral Blood ◽  
Oxidative Stress Response ◽  
Molecular Characteristics ◽  
Nuclear Factor ◽  
Normobaric Oxygen ◽  
Oxygen Paradox

The term “normobaric oxygen paradox” (NOP), describes the response to the return to normoxia after a hyperoxic event, sensed by tissues as oxygen shortage, and resulting in up-regulation of the Hypoxia-inducible factor 1α (HIF-1α) transcription factor activity. The molecular characteristics of this response have not been yet fully characterized. Herein, we report the activation time trend of oxygen-sensitive transcription factors in human peripheral blood mononuclear cells (PBMCs) obtained from healthy subjects after one hour of exposure to mild (MH), high (HH) and very high (VHH) hyperoxia, corresponding to 30%, 100%, 140% O2, respectively. Our observations confirm that MH is perceived as a hypoxic stress, characterized by the activation of HIF-1α and Nuclear factor (erythroid-derived 2)-like 2 (NRF2), but not Nuclear Factor kappa-light-chain-enhancer of activated B cells (NF-κB). Conversely, HH is associated to a progressive loss of NOP response and to an increase in oxidative stress leading to NRF2 and NF-kB activation, accompanied by the synthesis of glutathione (GSH). After VHH, HIF-1α activation is totally absent and oxidative stress response, accompanied by NF-κB activation, is prevalent. Intracellular GSH and Matrix metallopeptidase 9 (MMP-9) plasma levels parallel the transcription factors activation pattern and remain elevated throughout the observation time. In conclusion, our study confirms that, in vivo, the return to normoxia after MH is sensed as a hypoxic trigger characterized by HIF-1α activation. On the contrary, HH and VHH induce a shift toward an oxidative stress response, characterized by NRF2 and NF-κB activation in the first 24 h post exposure.

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 Physiological Implications of Hydrogen Sulfide in Plants: Pleasant Exploration behind Its Unpleasant Odour

2015 ◽  
Vol 2015 ◽  
pp. 1-6 ◽  
Author(s):  
Zhuping Jin ◽  
Yanxi Pei
Keyword(s):  
Hydrogen Sulfide ◽  
Growth And Development ◽  
Defense Responses ◽  
Plant Responses ◽  
Plant Growth And Development ◽  
Systematic Classification ◽  
Physiological Processes ◽  
Overwhelming Evidence

Recently, overwhelming evidence has proven that hydrogen sulfide (H2S), which was identified as a gasotransmitter in animals, plays important roles in diverse physiological processes in plants as well. With the discovery and systematic classification of the enzymes producing H2Sin vivo, a better understanding of the mechanisms by which H2S influences plant responses to various stimuli was reached. There are many functions of H2S, including the modulation of defense responses and plant growth and development, as well as the regulation of senescence and maturation. Additionally, mounting evidence indicates that H2S signaling interacts with plant hormones, hydrogen peroxide, nitric oxide, carbon monoxide, and other molecules in signaling pathways.

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 PredicTF: a tool to predict bacterial transcription factors in complex microbial communities

2021 ◽  
Author(s):  
Lummy Maria Oliveira Monteiro ◽  
Joao Saraiva ◽  
Rodolfo Brizola Toscan ◽  
Peter F Stadler ◽  
Rafael Silva-Rocha ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Microbial Communities ◽  
Open Source ◽  
Genetic Information ◽  
Environmental Isolate ◽  
Ammonium Oxidation ◽  
Cellular Gene ◽  
Bacterial Transcription

AbstractTranscription Factors (TFs) are proteins that control the flow of genetic information by regulating cellular gene expression. Here we describe PredicTF, a first platform supporting the prediction and classification of novel bacterial TF in complex microbial communities. We evaluated PredicTF using a two-step approach. First, we tested PredictTF’s ability to predict TFs for the genome of an environmental isolate. In the second evaluation step, PredicTF was used to predict TFs in a metagenome and 11 metatranscriptomes recovered from a community performing anaerobic ammonium oxidation (anammox) in a bioreactor. PredicTF is open source pipeline available at https://github.com/mdsufz/PredicTF.

The endocrine response to stress

2011 ◽  
pp. 287-294
Author(s):  
David E. Henley ◽  
Joey M. Kaye ◽  
Stafford L. Lightman
Keyword(s):  
Stress Response ◽  
Initial Exposure ◽  
Behavioural Responses ◽  
Physiological Processes ◽  
Psychological Stressors ◽  
Endocrine Stress Response ◽  
The Face ◽  
Response To Stress ◽  
Trauma Injury ◽  
As Stress

In the face of any threat or challenge, either real or perceived, an organism must mount a series of coordinated and specific hormonal, autonomic, immune, and behavioural responses that allow it to either escape or adapt (1–3). To be successful, the characteristics and intensity of the response must match that posed by the threat itself and should last no longer than is necessary. A response that is either inadequate or excessive in terms of its specificity, intensity or duration may result in one or more of a multitude of psychological or physical pathologies (2–5). This concept of threat and the organism’s response to it is frequently recognized and understood as ‘stress’ but is so diverse that it lacks a universally accepted definition (2) and thus is difficult to investigate or study (6). In the early 1900s, Walter Cannon introduced the concept of homoeostasis (4)—an ideal steady state for all physiological processes. Stress has been defined as the state where this ideal is threatened. More easily appreciated, however, are those factors, both intrinsic and extrinsic, which represent a challenge to homoeostasis (termed stressors) and the complex physiological, hormonal, and behavioural responses that occur to restore the balance, the stress response (1). The importance of endocrine systems in this stress response was emphasized by Hans Selye (7), who described the need for multiple, integrated systems to respond in a coordinated fashion following exposure to a particular stressor. Nonspecific activation of the hypothalamic–pituitary–adrenal (HPA) and sympatho-adrenomedullary (SAM) axes occurred following initial exposure to a noxious stimulus. Continued exposure to the same agent has been shown to have lasting and damaging effects on various endocrine, immune, and other systems, although recovery from this state was possible provided the stress was terminated (7). In addition to various noxious agents, numerous potential stressors exist including exertion, physical extremes, trauma, injury, and psychological stress. Indeed, psychological stressors are some of the most potent stimuli of the endocrine stress response particularly when they involve elements of novelty, uncertainty, and unpredictability. This has been highlighted by the observation that anticipating an event can be as potent an activator of the stress response as the event itself (7).

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