scholarly journals From Intracellular Bacteria to Differentiated Bacteroids: Transcriptome and Metabolome Analysis inAeschynomeneNodules Using theBradyrhizobiumsp. Strain ORS285bclAMutant

2019 ◽  
Vol 201 (17) ◽  
Author(s):  
Florian Lamouche ◽  
Anaïs Chaumeret ◽  
Ibtissem Guefrachi ◽  
Quentin Barrière ◽  
Olivier Pierre ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcriptome Analysis ◽  
Soil Bacteria ◽  
Regulation Of Gene Expression ◽  
Nitrogen Fertilizers ◽  
Peptide Transporter ◽  
Intracellular Bacteria ◽  
Nitrogen Fixing ◽  
Wild Type ◽  
Free Living

ABSTRACTSoil bacteria called rhizobia trigger the formation of root nodules on legume plants. The rhizobia infect these symbiotic organs and adopt an intracellular lifestyle within the nodule cells, where they differentiate into nitrogen-fixing bacteroids. Several legume lineages force their symbionts into an extreme cellular differentiation, comprising cell enlargement and genome endoreduplication. The antimicrobial peptide transporter BclA is a major determinant of this process inBradyrhizobiumsp. strain ORS285, a symbiont ofAeschynomenespp. In the absence of BclA, the bacteria proceed until the intracellular infection of nodule cells, but they cannot differentiate into enlarged polyploid and functional bacteroids. Thus, thebclAnodule bacteria constitute an intermediate stage between the free-living soil bacteria and the nitrogen-fixing bacteroids. Metabolomics on whole nodules ofAeschynomene afrasperaandAeschynomene indicainfected with the wild type or thebclAmutant revealed 47 metabolites that differentially accumulated concomitantly with bacteroid differentiation. Bacterial transcriptome analysis of these nodules demonstrated that the intracellular settling of the rhizobia in the symbiotic nodule cells is accompanied by a first transcriptome switch involving several hundred upregulated and downregulated genes and a second switch accompanying the bacteroid differentiation, involving fewer genes but ones that are expressed to extremely elevated levels. The transcriptomes further suggested a dynamic role for oxygen and redox regulation of gene expression during nodule formation and a nonsymbiotic function of BclA. Together, our data uncover the metabolic and gene expression changes that accompany the transition from intracellular bacteria into differentiated nitrogen-fixing bacteroids.IMPORTANCELegume-rhizobium symbiosis is a major ecological process, fueling the biogeochemical nitrogen cycle with reduced nitrogen. It also represents a promising strategy to reduce the use of chemical nitrogen fertilizers in agriculture, thereby improving its sustainability. This interaction leads to the intracellular accommodation of rhizobia within plant cells of symbiotic organs, where they differentiate into nitrogen-fixing bacteroids. In specific legume clades, this differentiation process requires the bacterial transporter BclA to counteract antimicrobial peptides produced by the host. Transcriptome analysis ofBradyrhizobiumwild-type andbclAmutant bacteria in culture and in symbiosis withAeschynomenehost plants dissected the bacterial transcriptional response in distinct phases and highlighted functions of the transporter in the free-living stage of the bacterial life cycle.

scholarly journals The nucleoplasmic interactions among Lamin A/C-pRB-LAP2α-E2F1 are modulated by dexamethasone

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Anastasia Ricci ◽  
Sara Orazi ◽  
Federica Biancucci ◽  
Mauro Magnani ◽  
Michele Menotta
Keyword(s):  
Gene Expression ◽  
Cell Cycle Progression ◽  
Regulation Of Gene Expression ◽  
Lamin A ◽  
Wild Type ◽  
Cycle Progression ◽  
C Dynamics ◽  
E2f Transcription Factor ◽  
Transcription Factor 1

AbstractAtaxia telangiectasia (AT) is a rare genetic neurodegenerative disease. To date, there is no available cure for the illness, but the use of glucocorticoids has been shown to alleviate the neurological symptoms associated with AT. While studying the effects of dexamethasone (dex) in AT fibroblasts, by chance we observed that the nucleoplasmic Lamin A/C was affected by the drug. In addition to the structural roles of A-type lamins, Lamin A/C has been shown to play a role in the regulation of gene expression and cell cycle progression, and alterations in the LMNA gene is cause of human diseases called laminopathies. Dex was found to improve the nucleoplasmic accumulation of soluble Lamin A/C and was capable of managing the large chromatin Lamin A/C scaffolds contained complex, thus regulating epigenetics in treated cells. In addition, dex modified the interactions of Lamin A/C with its direct partners lamin associated polypeptide (LAP) 2a, Retinoblastoma 1 (pRB) and E2F Transcription Factor 1 (E2F1), regulating local gene expression dependent on E2F1. These effects were differentially observed in both AT and wild type (WT) cells. To our knowledge, this is the first reported evidence of the role of dex in Lamin A/C dynamics in AT cells, and may represent a new area of research regarding the effects of glucocorticoids on AT. Moreover, future investigations could also be extended to healthy subjects or to other pathologies such as laminopathies since glucocorticoids may have other important effects in these contexts as well.

scholarly journals Alternative Oxidase Inhibition Impairs Tobacco Root Development and Root Hair Formation

2021 ◽  
Vol 12 ◽  
Author(s):  
Yang Liu ◽  
Lu-Lu Yu ◽  
Ye Peng ◽  
Xin-Xin Geng ◽  
Fei Xu
Keyword(s):  
Gene Expression ◽  
Root Development ◽  
Transcriptome Analysis ◽  
Root Hair ◽  
Alternative Oxidase ◽  
Regulation Of Gene Expression ◽  
Main Root ◽  
Respiratory Pathway ◽  
Root Hair Formation ◽  
Hair Formation

Alternative oxidase (AOX) is the terminal oxidase of the mitochondrial respiratory electron transport chain in plant cells and is critical for the balance of mitochondrial hemostasis. In this study, the effect of inhibition of AOX with different concentrations of salicylhydroxamic acid (SHAM) on the tobacco root development was investigated. We show here that AOX inhibition significantly impaired the development of the main root and root hair formation of tobacco. The length of the main root of SHAM-treated tobacco was significantly shorter than that of the control, and no root hairs were formed after treatment with a concentration of 1 mM SHAM or more. The transcriptome analysis showed that AOX inhibition by 1 mM SHAM involved in the regulation of gene expression related to root architecture. A total of 5,855 differentially expressed genes (DEGs) were obtained by comparing SHAM-treated roots with control. Of these, the gene expression related to auxin biosynthesis and perception were significantly downregulated by 1 mM SHAM. Similarly, genes related to cell wall loosening, cell cycle, and root meristem growth factor 1 (RGF1) also showed downregulation on SHAM treatment. Moreover, combined with the results of physiological measurements, the transcriptome analysis demonstrated that AOX inhibition resulted in excessive accumulation of reactive oxygen species in roots, which further induced oxidative damage and cell apoptosis. It is worth noting that when indoleacetic acid (20 nM) and dimethylthiourea (10 mM) were added to the medium containing SHAM, the defects of tobacco root development were alleviated, but to a limited extent. Together, these findings indicated that AOX-mediated respiratory pathway plays a crucial role in the tobacco root development, including root hair formation.

Factor XIII-A is involved in the regulation of gene expression in alternatively activated human macrophages

2010 ◽  
Vol 104 (10) ◽  
pp. 709-717 ◽  
Author(s):  
Dániel Töröcsik ◽  
Lajos Széles ◽  
György Paragh ◽  
Zsuzsa Rákosy ◽  
Helga Bárdos ◽  
...  
Keyword(s):  
Gene Expression ◽  
Factor Xiii ◽  
Gene Expression Regulation ◽  
Regulation Of Gene Expression ◽  
Wound Response ◽  
Interleukin 4 ◽  
Alternative Activation ◽  
Wild Type ◽  
Functional Clustering ◽  
Alternatively Activated

SummaryFactor XIII subunit A (FXIII-A) is one of the most overrepresented genes that is expressed during the alternative activation of macrophages. Based on its substrate profile and its cellular localisation, FXIII-A is thought to function as an intracellular/intranuclear transglutaminase. Our aim was to find role for the intracellular FXIII-A by comparing the microarray profiles of alternatively activated monocyte-derived macrophages. Microarray analyses of FXIII-A-deficient patients and healthy controls were evaluated, followed by functional clustering of the differentially expressed genes. After a 48-hour differentiation in the presence of interleukin 4 (IL4), 1,017 probes out of the 24,398 expressed in macrophages from FXIII-A- deficient samples were IL4 sensitive, while only 596 probes were IL4 sensitive in wild-type samples. Of these genes, 307 were induced in both the deficient and the wild-type macrophages. Our results revealed that FXIII-A has important role(s) in mediating gene expression changes in macrophages during alternative activation. Functional clustering of the target genes carried out using Cytoscape/BiNGO and Ingenuity Pathways Analysis programs showed that, in the absence of FXIII-A, the most prominent differences are related to immune functions and to wound response. Our findings suggest that functional impairment of macrophages at the level of gene expression regulation plays a role in the wound healing defects of FXIII-A-deficient patients.

scholarly journals Insights into the Noncoding RNome of Nitrogen-Fixing Endosymbiotic α-Proteobacteria

2013 ◽  
Vol 26 (2) ◽  
pp. 160-167 ◽  
Author(s):  
José I. Jiménez-Zurdo ◽  
Claudio Valverde ◽  
Anke Becker
Keyword(s):  
Gene Expression ◽  
Large Scale ◽  
Regulation Of Gene Expression ◽  
Living Environment ◽  
Large Set ◽  
Nitrogen Fixing ◽  
Symbiotic Interaction ◽  
Animal Pathogens ◽  
Wide Range ◽  
The Impact

Symbiotic chronic infection of legumes by rhizobia involves transition of invading bacteria from a free-living environment in soil to an intracellular state as differentiated nitrogen-fixing bacteroids within the nodules elicited in the host plant. The adaptive flexibility demanded by this complex lifestyle is likely facilitated by the large set of regulatory proteins encoded by rhizobial genomes. However, proteins are not the only relevant players in the regulation of gene expression in bacteria. Large-scale high-throughput analysis of prokaryotic genomes is evidencing the expression of an unexpected plethora of small untranslated transcripts (sRNAs) with housekeeping or regulatory roles. sRNAs mostly act in response to environmental cues as post-transcriptional regulators of gene expression through protein-assisted base-pairing interactions with target mRNAs. Riboregulation contributes to fine-tune a wide range of bacterial processes which, in intracellular animal pathogens, largely compromise virulence traits. Here, we summarize the incipient knowledge about the noncoding RNome structure of nitrogen-fixing endosymbiotic bacteria as inferred from genome-wide searches for sRNA genes in the alfalfa partner Sinorhizobium meliloti and further comparative genomics analysis. The biology of relevant S. meliloti RNA chaperones (e.g., Hfq) is also reviewed as a first global indicator of the impact of riboregulation in the establishment of the symbiotic interaction.

scholarly journals Gene Expression and Regulation from the p7 Promoter of Aedes Densonucleosis Virus

1998 ◽  
Vol 72 (5) ◽  
pp. 4364-4370 ◽  
Author(s):  
Michael W. Kimmick ◽  
Boris N. Afanasiev ◽  
Barry J. Beaty ◽  
Jonathan O. Carlson
Keyword(s):  
Gene Expression ◽  
Translational Regulation ◽  
Transcriptional Control ◽  
Regulation Of Gene Expression ◽  
Open Reading Frames ◽  
Gene Expression And Regulation ◽  
Wild Type ◽  
Nonstructural Proteins ◽  
Study Gene Expression ◽  
Reading Frames

ABSTRACT The nonstructural proteins NS1 and NS2 are thought to be expressed from the p7 promoter of Aedes densonucleosis virus (AeDNV). To study gene expression from the p7 promoter, eight different plasmids were constructed by fusing β-galactosidase or β-glucuronidase into the genome so that the reporter gene was in different open reading frames and under the transcriptional control of the p7 promoter. After transfection into C6/36 Aedes albopictus cells, constructs generated comparable amounts of RNA, but only the NS1 and NS2 fusion constructs produced appreciable levels of active enzyme. NS1 and NS2 fusion constructs contained wild-type AeDNV sequences from the p7 promoter downstream to nucleotide 458. The remaining constructs, with the exception of p7GUS.rf3, lacked some or all of these necessary sequences and inefficiently produced protein. These data suggest that sequences downstream of the p7 promoter play a role in translational regulation of gene expression from the p7 promoter of AeDNV.

scholarly journals Genome Architecture of the Human β-Globin Locus Affects Developmental Regulation of Gene Expression

2005 ◽  
Vol 25 (20) ◽  
pp. 8765-8778 ◽  
Author(s):  
Susanna Harju ◽  
Patrick A. Navas ◽  
George Stamatoyannopoulos ◽  
Kenneth R. Peterson
Keyword(s):  
Gene Expression ◽  
Gene Order ◽  
Yeast Artificial Chromosome ◽  
Fetal Liver ◽  
Globin Gene ◽  
Regulation Of Gene Expression ◽  
Globin Genes ◽  
Wild Type ◽  
Globin Mrna ◽  
Definitive Erythropoiesis

ABSTRACT To test the role of gene order in globin gene expression, mutant human β-globin locus yeast artificial chromosome constructs were used, each having one additional globin gene encoding a “marked” transcript (εm, γm, or βm) integrated at different locations within the locus. When a βm-globin gene was placed between the locus control region (LCR) and the ε-globin gene, βm-globin expression dominated primitive and definitive erythropoiesis; only βm-globin mRNA was detected during the fetal and adult definitive stages of erythropoiesis. When an Aγm-globin gene was placed at the same location, Aγm-globin was expressed during embryonic erythropoiesis and the fetal liver stage of definitive erythropoiesis but was silenced during the adult stage. The downstream wild-type γ-globin genes were not expressed. When an εm-globin gene was placed between the δ- and β-globin genes, it remained silent during embryonic erythropoiesis; only the LCR-proximal wild-type ε-globin gene was expressed. Placement of a βm-globin gene upstream of the Gγ-globin gene resulted in expression of βm-globin in embryonic cells and in a significant decrease in expression of the downstream wild-type β-globin gene. These results indicate that distance from the LCR, an inherent property of spatial gene order, is a major determinant of temporal gene expression during development.

scholarly journals RNase L Is Involved in Liposaccharide-Induced Lung Inflammation

Viruses ◽  
2020 ◽  
Vol 12 (1) ◽  
pp. 73
Author(s):  
Ruhan Wei ◽  
Guanmin Chen ◽  
Naseh Algehainy ◽  
Chun Zeng ◽  
Chunfang Liu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Immune Response ◽  
Cell Proliferation ◽  
Acute Lung Injury ◽  
Lung Inflammation ◽  
Regulation Of Gene Expression ◽  
Rnase L ◽  
Wild Type ◽  
Tlr4 Signaling Pathway

RNase L mediates interferon (IFN) function during viral infection and cell proliferation. Furthermore, the role of RNase L in the regulation of gene expression, cell apoptosis, autophagy, and innate immunity has been well established in the last decade. Tissue distribution reveals that RNase L is highly expressed in the lung and other organs. However, the physiological roles of RNase L in the lung are largely unknown. In this study, we found that polysaccharide (LPS)-induced acute lung injury (ALI) was remarkably intensified in mice deficient in RNase L compared to wild type mice under the same condition. Furthermore, we found that RNase L mediated the TLR4 signaling pathway, and regulated the expression of various pro- and anti-inflammatory genes in the lung tissue and blood. Most importantly, RNase L function in macrophages during LPS stimulation may be independent of the 2-5A system. These findings demonstrate a novel role of RNase L in the immune response via an atypical molecular mechanism.

scholarly journals Wild-type p53 mediates positive regulation of gene expression through a specific DNA sequence element.

1992 ◽  
Vol 6 (7) ◽  
pp. 1143-1152 ◽  
Author(s):  
G P Zambetti ◽  
J Bargonetti ◽  
K Walker ◽  
C Prives ◽  
A J Levine
Keyword(s):  
Gene Expression ◽  
Dna Sequence ◽  
Regulation Of Gene Expression ◽  
Wild Type ◽  
Positive Regulation ◽  
Sequence Element ◽  
Wild Type P53

scholarly journals Azorhizobium caulinodans PIIand GlnK Proteins Control Nitrogen Fixation and Ammonia Assimilation

1999 ◽  
Vol 181 (8) ◽  
pp. 2655-2658 ◽  
Author(s):  
Nathalie Michel-Reydellet ◽  
P. Alexandre Kaminski
Keyword(s):  
Gene Expression ◽  
Nitrogen Fixation ◽  
Nitrogenase Activity ◽  
Ammonia Assimilation ◽  
Ammonium Excretion ◽  
Azorhizobium Caulinodans ◽  
Wild Type ◽  
Free Living ◽  
Living State ◽  
High Level

ABSTRACT We herein report that Azorhizobium caulinodansPII and GlnK are not necessary for glutamine synthetase (GS) adenylylation whereas both proteins are required for complete GS deadenylylation. The disruption of both glnB andglnK resulted in a high level of GS adenylylation under the condition of nitrogen fixation, leading to ammonium excretion in the free-living state. PII and GlnK also controllednif gene expression because NifA activated nifHtranscription and nitrogenase activity was derepressed in glnB glnK double mutants, but not in wild-type bacteria, grown in the presence of ammonia.

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