scholarly journals Search for Candidate Genes Causing the Excessive Ca Accumulation in Roots of Tipburn-Damaged Lisianthus (Eustoma grandiflorum) Cultivars

Agriculture ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 254
Author(s):  
Takanori Kuronuma ◽  
Hitoshi Watanabe
Keyword(s):  
Gene Expression ◽  
Candidate Genes ◽  
Target Genes ◽  
Pectin Methylesterase ◽  
Eustoma Grandiflorum ◽  
Gene Encoding ◽  
Severe Problem ◽  
Horticultural Crops ◽  
Genes Encoding ◽  
Leaves And Roots

Occurrence of tipburn is a severe problem in the production of lisianthus cultivars. Previous studies have shown excessive Ca accumulation in the roots of tipburn-damaged cultivars, where the distribution of Ca to the tips of the top leaves is inhibited. However, few studies have investigated the association between Ca accumulation and gene expression in horticultural crops. To provide a list of candidate target genes that might be causing the excessive Ca accumulation in roots, we focused Ca2+ transporter and pectin methylesterase (PME) genes and RNA-seq of upper leaves and roots in tipburn-occurrence cultivar (“Voyage peach”: VP) and non-occurrence cultivar (“Umi honoka”: UH) was conducted. In both the upper leaves and roots of VP, genes encoding the glutamate receptors (GLRs), cation/Ca2+ exchangers 4 (CCX4), Na+/Ca2+ exchanger-like protein (NCL), and PMEs were upregulated, and a gene encoding the cyclic nucleotide-gated ion channel 9 (CNGC9) was downregulated. In contrast, genes encoding the vacuolar cation/proton exchanger 5 (CAX5), calcium-transporting ATPase 1 and 12 (ACA1 and ACA12) showed differential expression in each organ. Among them, only CAX5 was upregulated and ACA12 was downregulated in the roots of VP. Based on these results, we suggested that CAX5 and ACA12 are the candidate genes causing the excessive Ca accumulation in the roots of tipburn-occurrence lisianthus cultivars. Future studies should investigate the temporal changes in gene expression using quantitative PCR and conduct functional analysis of candidate genes in tipburn-damaged lisianthus cultivars.

scholarly journals RNA Interference of Genes Encoding the Vacuolar-ATPase in Liriomyza trifolii

Insects ◽  
2021 ◽  
Vol 12 (1) ◽  
pp. 41
Author(s):  
Ya-Wen Chang ◽  
Yu-Cheng Wang ◽  
Xiao-Xiang Zhang ◽  
Junaid Iqbal ◽  
Yu-Zhou Du
Keyword(s):  
Rna Interference ◽  
Expression Analysis ◽  
Target Genes ◽  
Fluorescent Protein ◽  
Control Strategies ◽  
Vacuolar Atpase ◽  
Invasive Pest ◽  
Liriomyza Trifolii ◽  
Horticultural Crops ◽  
Genes Encoding

The leafminer fly, Liriomyza trifolii, is an invasive pest of vegetable and horticultural crops in China. In this study, a microinjection method based on dsRNA was developed for RNA interference (RNAi) in L. trifolii using genes encoding vacuolar-ATPase (V-ATPase). Expression analysis indicated that V-ATPase B and V-ATPase D were more highly expressed in L. trifolii adults than in larvae or pupae. Microinjection experiments with dsV-ATPase B and dsV-ATPase D were conducted to evaluate the efficacy of RNAi in L. trifolii adults. Expression analysis indicated that microinjection with 100 ng dsV-ATPase B or dsV-ATPase led to a significant reduction in V-ATPase transcripts as compared to that of the dsGFP control (dsRNA specific to green fluorescent protein). Furthermore, lower dsRNA concentrations were also effective in reducing the expression of target genes when delivered by microinjection. Mortality was significantly higher in dsV-ATPase B- and dsV-ATPase D-treated insects than in controls injected with dsGFP. The successful deployment of RNAi in L. trifolii will facilitate functional analyses of vital genes in this economically-important pest and may ultimately result in new control strategies.

scholarly journals NRF2 and the Ambiguous Consequences of Its Activation during Initiation and the Subsequent Stages of Tumourigenesis

Cancers ◽  
2020 ◽  
Vol 12 (12) ◽  
pp. 3609
Author(s):  
Holly Robertson ◽  
Albena T. Dinkova-Kostova ◽  
John D. Hayes
Keyword(s):  
Somatic Mutations ◽  
Target Genes ◽  
Cancer Chemoprevention ◽  
Chemical Carcinogenesis ◽  
Related Factor ◽  
Gene Encoding ◽  
Ubiquitin Ligase Complex ◽  
Genes Encoding ◽  
Short Term Adaptation ◽  
Cullin 3

NF-E2 p45-related factor 2 (NRF2, encoded in the human by NFE2L2) mediates short-term adaptation to thiol-reactive stressors. In normal cells, activation of NRF2 by a thiol-reactive stressor helps prevent, for a limited period of time, the initiation of cancer by chemical carcinogens through induction of genes encoding drug-metabolising enzymes. However, in many tumour types, NRF2 is permanently upregulated. In such cases, its overexpressed target genes support the promotion and progression of cancer by suppressing oxidative stress, because they constitutively increase the capacity to scavenge reactive oxygen species (ROS), and they support cell proliferation by increasing ribonucleotide synthesis, serine biosynthesis and autophagy. Herein, we describe cancer chemoprevention and the discovery of the essential role played by NRF2 in orchestrating protection against chemical carcinogenesis. We similarly describe the discoveries of somatic mutations in NFE2L2 and the gene encoding the principal NRF2 repressor, Kelch-like ECH-associated protein 1 (KEAP1) along with that encoding a component of the E3 ubiquitin-ligase complex Cullin 3 (CUL3), which result in permanent activation of NRF2, and the recognition that such mutations occur frequently in many types of cancer. Notably, mutations in NFE2L2, KEAP1 and CUL3 that cause persistent upregulation of NRF2 often co-exist with mutations that activate KRAS and the PI3K-PKB/Akt pathway, suggesting NRF2 supports growth of tumours in which KRAS or PKB/Akt are hyperactive. Besides somatic mutations, NRF2 activation in human tumours can occur by other means, such as alternative splicing that results in a NRF2 protein which lacks the KEAP1-binding domain or overexpression of other KEAP1-binding partners that compete with NRF2. Lastly, as NRF2 upregulation is associated with resistance to cancer chemotherapy and radiotherapy, we describe strategies that might be employed to suppress growth and overcome drug resistance in tumours with overactive NRF2.

scholarly journals Hierarchical Regulation of Photosynthesis Gene Expression by the Oxygen-Responsive PrrBA and AppA-PpsR Systems of Rhodobacter sphaeroides

2008 ◽  
Vol 190 (24) ◽  
pp. 8106-8114 ◽  
Author(s):  
Larissa Gomelsky ◽  
Oleg V. Moskvin ◽  
Rachel A. Stenzel ◽  
Denise F. Jones ◽  
Timothy J. Donohue ◽  
...  
Keyword(s):  
Gene Expression ◽  
Rhodobacter Sphaeroides ◽  
Response Regulator ◽  
Photosynthetic Apparatus ◽  
Regulatory System ◽  
Structural Proteins ◽  
Gene Encoding ◽  
Genes Encoding ◽  
Photosynthetic Complexes ◽  
Photosynthesis Gene

ABSTRACT In the facultatively phototrophic proteobacterium Rhodobacter sphaeroides, formation of the photosynthetic apparatus is oxygen dependent. When oxygen tension decreases, the response regulator PrrA of the global two-component PrrBA system is believed to directly activate transcription of the puf, puh, and puc operons, encoding structural proteins of the photosynthetic complexes, and to indirectly upregulate the photopigment biosynthesis genes bch and crt. Decreased oxygen also results in inactivation of the photosynthesis-specific repressor PpsR, bringing about derepression of the puc, bch, and crt operons. We uncovered a hierarchical relationship between these two regulatory systems, earlier thought to function independently. We also more accurately assessed the spectrum of gene targets of the PrrBA system. First, expression of the appA gene, encoding the PpsR antirepressor, is PrrA dependent, which establishes one level of hierarchical dominance of the PrrBA system over AppA-PpsR. Second, restoration of the appA transcript to the wild-type level is insufficient for rescuing phototrophic growth impairment of the prrA mutant, whereas inactivation of ppsR is sufficient. This suggests that in addition to controlling appA transcription, PrrA affects the activity of the AppA-PpsR system via an as yet unidentified mechanism(s). Third, PrrA directly activates several bch and crt genes, traditionally considered to be the PpsR targets. Therefore, in R. sphaeroides, the global PrrBA system regulates photosynthesis gene expression (i) by rigorous control over the photosynthesis-specific AppA-PpsR regulatory system and (ii) by extensive direct transcription activation of genes encoding structural proteins of photosynthetic complexes as well as genes encoding photopigment biosynthesis enzymes.

scholarly journals Adaptation of Porphyromonas gingivalis to microaerophilic conditions involves increased consumption of formate and reduced utilization of lactate

Microbiology ◽  
2009 ◽  
Vol 155 (11) ◽  
pp. 3758-3774 ◽  
Author(s):  
Janina P. Lewis ◽  
Divya Iyer ◽  
Cecilia Anaya-Bergman
Keyword(s):  
Gene Expression ◽  
Porphyromonas Gingivalis ◽  
Model Organism ◽  
Oxygen Metabolism ◽  
Exponential Growth Phase ◽  
Transcriptional Level ◽  
Gene Encoding ◽  
Aerobic Conditions ◽  
Small Proteins ◽  
Genes Encoding

Porphyromonas gingivalis, previously classified as a strict anaerobe, can grow in the presence of low concentrations of oxygen. Microarray analysis revealed alteration in gene expression in the presence of 6 % oxygen. During the exponential growth phase, 96 genes were upregulated and 79 genes were downregulated 1.4-fold. Genes encoding proteins that play a role in oxidative stress protection were upregulated, including alkyl hydroperoxide reductase (ahpCF), superoxide dismutase (sod) and thiol peroxidase (tpx). Significant changes in gene expression of proteins that mediate oxidative metabolism, such as cytochrome d ubiquinol oxidase-encoding genes, cydA and cydB, were detected. The expression of genes encoding formate uptake transporter (PG0209) and formate tetrahydrofolate ligase (fhs) was drastically elevated, which indicates that formate metabolism plays a major role under aerobic conditions. The concomitant reduction of expression of a gene encoding the lactate transporter PG1340 suggests decreased utilization of this nutrient. The concentrations of both formate and lactate were assessed in culture supernatants and cells, and they were in agreement with the results obtained at the transcriptional level. Also, genes encoding gingipain protease secretion/maturation regulator (porR) and protease transporter (porT) had reduced expression in the presence of oxygen, which also correlated with reduced protease activities under aerobic conditions. In addition, metal transport was affected, and while iron-uptake genes such as the genes encoding the haemin uptake locus (hmu) were downregulated, expression of manganese transporter genes, such as feoB2, was elevated in the presence of oxygen. Finally, genes encoding putative regulatory proteins such as extracellular function (ECF) sigma factors as well as small proteins had elevated expression levels in the presence of oxygen. As P. gingivalis is distantly related to the well-studied model organism Escherichia coli, results from our work may provide further understanding of oxygen metabolism and protection in other related bacteria belonging to the phylum Bacteroidetes.

scholarly journals Metabolic Signals That Lead to Control of CBB Gene Expression in Rhodobacter capsulatus

2002 ◽  
Vol 184 (7) ◽  
pp. 1905-1915 ◽  
Author(s):  
Mary A. Tichi ◽  
F. Robert Tabita
Keyword(s):  
Gene Expression ◽  
Rhodobacter Capsulatus ◽  
Pentose Phosphate ◽  
Gene Encoding ◽  
Bisphosphate Carboxylase ◽  
Starting Point ◽  
Mutant Strains ◽  
Genes Encoding ◽  
Metabolic Signal ◽  
Made In

ABSTRACT Various mutant strains were used to examine the regulation and metabolic control of the Calvin-Benson-Bassham (CBB) reductive pentose phosphate pathway in Rhodobacter capsulatus. Previously, a ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO)-deficient strain (strain SBI/II) was found to show enhanced levels of cbb I and cbb II promoter activities during photoheterotrophic growth in the presence of dimethyl sulfoxide. With this strain as the starting point, additional mutations were made in genes encoding phosphoribulokinase and transketolase and in the gene encoding the LysR-type transcriptional activator, CbbRII. These strains revealed that a product generated by phosphoribulokinase was involved in control of CbbR-mediated cbb gene expression in SBI/II. Additionally, heterologous expression experiments indicated that Rhodobacter sphaeroides CbbR responded to the same metabolic signal in R. capsulatus SBI/II and mutant strain backgrounds.

scholarly journals CRUP: A comprehensive framework to predict condition-specific regulatory units

2018 ◽  
Author(s):  
Anna Ramisch ◽  
Verena Heinrich ◽  
Laura V. Glaser ◽  
Alisa Fuchs ◽  
Xinyi Yang ◽  
...  
Keyword(s):  
Rheumatoid Arthritis ◽  
Gene Expression ◽  
Histone Modification ◽  
Candidate Genes ◽  
Cell Lines ◽  
Target Genes ◽  
Disease Genes ◽  
Epigenetic Marks ◽  
Arthritis Model ◽  
Comprehensive Framework

AbstractWe present the software CRUP (Condition-specific Regulatory Units Prediction) to infer from epigenetic marks a list of regulatory units consisting of dynamically changing enhancers with their target genes. The workflow consists of a novel pre-trained enhancer predictor that can be reliably applied across cell lines and species, solely based on histone modification ChIP-seq data. Enhancers are subsequently assigned to different conditions and correlated with gene expression to derive regulatory units. We thoroughly test and then apply CRUP to a rheumatoid arthritis model, identifying enhancer-gene pairs comprising known disease genes as well as new candidate genes.Availabilityhttps://github.com/VerenaHeinrich/CRUP

Pbx-1 Is a Direct Target of Evi-1 in Hematopoietic Stem/Progenitors and Leukemic Cells.

Blood ◽  
2008 ◽  
Vol 112 (11) ◽  
pp. 1192-1192
Author(s):  
Munetake Shimabe ◽  
Susumu Goyama ◽  
Motoshi Ichikawa ◽  
Yoichi Imai ◽  
Tsuyoshi Takahashi ◽  
...  
Keyword(s):  
Gene Expression ◽  
Stem Cells ◽  
Bone Marrow ◽  
Hematopoietic Stem Cells ◽  
Candidate Genes ◽  
Zinc Finger ◽  
Target Genes ◽  
Leukemic Cells ◽  
Hematopoietic Stem ◽  
Direct Target

Abstract The ecotropic viral integration site-1 (Evi-1) gene was first identified as a common locus of retroviral integration in murine leukemia. In humans, Evi-1 is located on chromosome 3q26, and rearrangements on chrmosome 3q26 often activate Evi-1 expression in acute myeloid leukemia (AML) and myelodysplastic syndrome (MDS). Patients with these karyotypes are characterized by the elevated platelet count and lack of response to antileukemic therapy. Elevated Evi-1 expression occurs with high frequency in AML patients without 3q26 abnormalities, and is also associated with unfavorable outcomes. Thus, Evi-1 is one of the key factors that predict poor survival in leukemia patients. Evi-1 is a member of the SET/PR domain family of transcription factors and it contains a total of 10 zinc finger motifs organized in two discrete domains, comprising 7 and 3 repeats respectively, which have distinct DNA binding specificities. Recently, we generated Evi-1-mutant mice and showed that Evi-1 plays an essential role in proliferation of both hematopoietic stem cells (HSCs) and transformed leukemic cells. Furthermore, we identified candidate target genes of Evi-1 using gene expression profiling analysis in HSCs combined with the gene expression data of AML samples. These genes include Gata1, Gata2, Angpt1, Mpl, Jag2, Pbx-1, Setbp1 and Itga2b. In this study, we first analyzed relative gene expression of these candidate genes in control- or Evi-1-transduced hematopoietic stem/progenitors (c-Kit+ cells). Among these candidate genes, Evi-1 up-regulates transcription of Pbx-1, Mpl, Setbp1 and Itga2b. Next, we cloned 5 ′ up-stream genomic regions of these four genes into the pGL-4 luciferase reporter vector, and found that Evi-1 increased luciferase activity of Pbx-1 reporter construct in COS7 cells. Deletion of reporter constructs revealed that Evi-1 binds to -0.5kb upstream of the transcription start site of Pbx-1. We then examined the transcription activity of a series of Evi-1 mutants and found that both the first and second zinc finger domains are required for the Pbx-1 up-regulation. Furthermore, chromatin immunoprecipitation (ChIP) analysis revealed that Evi-1 directly binds to the promoter region of Pbx-1. We next evaluated a role for Pbx-1 in Evi-1-induced myeloid transformation. Bone marrow progenitors transduced with Evi-1 showed sustained colony formation in the serial replating assay. After establishment of sustained clonogenic activity following more than three rounds of replating in methylcellulose medium, the cells were transduced with control or Pbx-1-shRNA. Interestingly, reduction of Pbx-1 levels through RNAi-mediated knockdown significantly inhibited Evi-1-induced transformation. In contrast, knockdown of Pbx-1 did not impair bone marrow transformation by transcription factor E2A-hepatic leukemia factor (E2A-HLF), suggesting that Pbx-1 is specifically, as opposed to generally, required for maintenance of transformation mediated by Evi-1. Taken together, these results indicate that Pbx-1 is one of the direct target genes of Evi- 1 in hematopoietic cells, and aberrant Pbx-1 expression is responsible, at least in part, for the oncogenic activity of Evi-1. Because Pbx-1 is known as a critical regulator of hematopoietic stem cells and leukemia development, the Evi-1-Pbx-1 pathway may be a key modulator of stem cell activity in normal and malignant hematopoiesis.

scholarly journals Tissue-Specific Transgenic Knockdown of Fos-Related Antigen 2 (Fra-2) Expression Mediated by Dominant Negative Fra-2

2001 ◽  
Vol 21 (11) ◽  
pp. 3704-3713 ◽  
Author(s):  
Martin Smith ◽  
Zoe Burke ◽  
Ann Humphries ◽  
Tim Wells ◽  
David Klein ◽  
...  
Keyword(s):  
Gene Expression ◽  
Pineal Gland ◽  
Target Genes ◽  
Second Messengers ◽  
Regulatory Region ◽  
Dominant Negative ◽  
Transgenic Rat ◽  
Iodothyronine Deiodinase ◽  
Protein Levels ◽  
Genes Encoding

ABSTRACT Fos-related antigen 2 (Fra-2) is a member of the Fos family of immediate-early genes, most of which are rapidly induced by second messengers. All members of this family act by binding to AP-1 sites as heterodimeric complexes with other proteins. However, each appears to have a distinct role. The role and biology of Fra-2 are less well understood than those of its relatives c-Fos, Fra-1, and FosB; moreover, Fra-2 target genes remain largely unknown, as does the basis of its selective effects on transcriptional activity. To pursue these issues, we created a transgenic rat line (NATDNF2) in which a dominant negative fra-2 (DNF2) gene is strongly expressed in the pineal gland; tissue selectivity was achieved by putting the DNF2 gene under the control of the rat arylalkylamineN-acetyltransferase (AANAT) regulatory region, which targets gene expression to a very restricted set of tissues (pineal gland ≫ retina). Expression of AANAT is normally turned on after the onset of darkness in the rat; as a result, pineal DNF2 expression occurs only at night. This was associated with marked suppression of the nocturnal increase in fra-2 mRNA and protein levels, indicating that DNF2 expression inhibits downstream effects of Fra-2, including the maintenance of high levels offra-2 gene expression. Analysis of 1,190 genes in the NATDNF2 pineal gland, including the AANAT gene, identified two whose expression is strongly linked to fra-2 expression: the genes encoding type II iodothyronine deiodinase and nectadrin (CD24).

scholarly journals Identification of Three Genes Encoding PII-Like Proteins in Gluconacetobacter diazotrophicus: Studies of Their Role(s) in the Control of Nitrogen Fixation

2003 ◽  
Vol 185 (19) ◽  
pp. 5854-5861 ◽  
Author(s):  
Olena Perlova ◽  
Alejandro Ureta ◽  
Stefan Nordlund ◽  
Dietmar Meletzus
Keyword(s):  
Gene Expression ◽  
Nitrogen Fixation ◽  
Gluconacetobacter Diazotrophicus ◽  
Triple Mutant ◽  
Gene Encoding ◽  
Protein Encoding ◽  
Genes Encoding ◽  
Encoding Gene ◽  
Encoding Genes ◽  
Expression And Activity

ABSTRACT In our studies on the regulation of nitrogen metabolism in Gluconacetobacter diazotrophicus, an endophytic diazotroph of sugarcane, three glnB-like genes were identified and their role(s) in the control of nitrogen fixation was studied. Sequence analysis revealed that one PII protein-encoding gene, glnB, was adjacent to a glnA gene (encoding glutamine synthetase) and that two other PII protein-encoding genes, identified as glnK1 and glnK2, were located upstream of amtB1 and amtB2, respectively, genes which in other organisms encode ammonium (or methylammonium) transporters. Single and double mutants and a triple mutant with respect to the three PII protein-encoding genes were constructed, and the effects of the mutations on nitrogenase expression and activity in the presence of either ammonium starvation or ammonium sufficiency were studied. Based on the results presented here, it is suggested that none of the three PII homologs is required for nif gene expression, that the GlnK2 protein acts primarily as an inhibitor of nif gene expression, and that GlnB and GlnK1 control the expression of nif genes in response to ammonium availability, both directly and by relieving the inhibition by GlnK2. This model includes novel regulatory features of PII proteins.

scholarly journals Obesity and Race Alter Gene Expression in Skin

2020 ◽  
Author(s):  
Jeanne M. Walker ◽  
Sandra Garcet ◽  
Jose O. Aleman ◽  
Christopher E. Mason ◽  
David Danko ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cystic Fibrosis ◽  
African Americans ◽  
Normal Weight ◽  
Gene Encoding ◽  
Functional Changes ◽  
Expression Of Genes ◽  
Genes Encoding ◽  
Expression Pathways ◽  
Altered Gene

ABSTRACTObesity is accompanied by dysfunction of many organs, but effects on the skin have received little attention. We studied differences in epithelial thickness by histology and gene expression by Affymetrix gene arrays and PCR in the skin of 10 obese (BMI 35-50) and 10 normal weight (BMI 18.5-26.9) postmenopausal women paired by age and race. Epidermal thickness did not differ with obesity but the expression of genes encoding proteins associated with skin blood supply and wound healing were altered. In the obese, many gene expression pathways were broadly downregulated and subdermal fat showed pronounced inflammation. There were no changes in skin microbiota or metabolites. African American subjects differed from Caucasians with a trend to increased epidermal thickening. In obese African Americans, compared to obese Caucasians, we observed altered gene expression that may explain known differences in water content and stress response. African Americans showed markedly lower expression of the gene encoding the cystic fibrosis transmembrane regulator characteristic of the disease cystic fibrosis. The results from this preliminary study may explain the functional changes found in the skin of obese subjects and African Americans.

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