scholarly journals The CCR4-NOT Complex Maintains Stability and Transcription of rRNA Genes by Repressing Antisense Transcripts

2019 ◽  
Vol 40 (1) ◽  
Author(s):  
Shun Hosoyamada ◽  
Mariko Sasaki ◽  
Takehiko Kobayashi
Keyword(s):  
Gene Expression ◽  
Enzymatic Activity ◽  
Noncoding Rna ◽  
Gene Clusters ◽  
Rrna Genes ◽  
Deletion Mutants ◽  
Antisense Transcripts ◽  
Content Type ◽  
A Subunit ◽  
By Products

ABSTRACT The rRNA genes (rDNA) in eukaryotes are organized into highly repetitive gene clusters. Each organism maintains a particular number of copies, suggesting that the rDNA is actively stabilized. We previously identified about 700 Saccharomyces cerevisiae genes that could contribute to rDNA maintenance. Here, we further analyzed these deletion mutants with unstable rDNA by measuring the amounts of extrachromosomal rDNA circles (ERCs) that are released as by-products of intrachromosomal recombination. We found that extremely high levels of ERCs were formed in the absence of Pop2 (Caf1), which is a subunit of the CCR4-NOT complex, important for the regulation of all stages of gene expression. In the pop2 mutant, transcripts from the noncoding promoter E-pro in the rDNA accumulated, and the amounts of cohesin and condensin were reduced, which could promote recombination events. Moreover, we discovered that the amount of rRNA was decreased in the pop2 mutant. Similar phenotypes were observed in the absence of subunits Ccr4 and Not4 that, like Pop2, convey enzymatic activity to the complex. These findings indicate that lack of any CCR4-NOT-associated enzymatic activity resulted in a severe unstable rDNA phenotype related to the accumulation of noncoding RNA from E-pro.

scholarly journals Methanobactin from Methylocystis sp. Strain SB2 Affects Gene Expression and Methane Monooxygenase Activity in Methylosinus trichosporium OB3b

2015 ◽  
Vol 81 (7) ◽  
pp. 2466-2473 ◽  
Author(s):  
Muhammad Farhan Ul-Haque ◽  
Bhagyalakshmi Kalidass ◽  
Alexey Vorobev ◽  
Bipin S. Baral ◽  
Alan A. DiSpirito ◽  
...  
Keyword(s):  
Gene Expression ◽  
Methane Monooxygenase ◽  
Particulate Methane Monooxygenase ◽  
Methylosinus Trichosporium Ob3b ◽  
Methylosinus Trichosporium ◽  
Monooxygenase Activity ◽  
Content Type ◽  
Soluble Methane Monooxygenase ◽  
A Subunit ◽  
Membrane Bound

ABSTRACTMethanotrophs can express a cytoplasmic (soluble) methane monooxygenase (sMMO) or membrane-bound (particulate) methane monooxygenase (pMMO). Expression of these MMOs is strongly regulated by the availability of copper. Many methanotrophs have been found to synthesize a novel compound, methanobactin (Mb), that is responsible for the uptake of copper, and methanobactin produced byMethylosinus trichosporiumOB3b plays a key role in controlling expression of MMO genes in this strain. As all known forms of methanobactin are structurally similar, it was hypothesized that methanobactin from one methanotroph may alter gene expression in another. WhenMethylosinus trichosporiumOB3b was grown in the presence of 1 μM CuCl2, expression ofmmoX, encoding a subunit of the hydroxylase component of sMMO, was very low.mmoXexpression increased, however, when methanobactin fromMethylocystissp. strain SB2 (SB2-Mb) was added, as did whole-cell sMMO activity, but there was no significant change in the amount of copper associated withM. trichosporiumOB3b. IfM. trichosporiumOB3b was grown in the absence of CuCl2, themmoXexpression level was high but decreased by several orders of magnitude if copper prebound to SB2-Mb (Cu-SB2-Mb) was added, and biomass-associated copper was increased. Exposure ofMethylosinus trichosporiumOB3b to SB2-Mb had no effect on expression ofmbnA, encoding the polypeptide precursor of methanobactin in either the presence or absence of CuCl2.mbnAexpression, however, was reduced when Cu-SB2-Mb was added in both the absence and presence of CuCl2. These data suggest that methanobactin acts as a general signaling molecule in methanotrophs and that methanobactin “piracy” may be commonplace.

Thymidine kinase activation of ganciclovir in recurrent malignant gliomas: a gene-marking and neuropathological study

2000 ◽  
Vol 92 (5) ◽  
pp. 804-811 ◽  
Author(s):  
Griffith R. Harsh ◽  
Thomas S. Deisboeck ◽  
David N. Louis ◽  
John Hilton ◽  
Michael Colvin ◽  
...  
Keyword(s):  
Gene Expression ◽  
Enzymatic Activity ◽  
Thymidine Kinase ◽  
Tumor Cells ◽  
Malignant Gliomas ◽  
Retroviral Vectors ◽  
Content Type ◽  
Tumor Bed ◽  
Immunohistochemical Evidence ◽  
Fine Print

Object. The gene therapy paradigm of intratumoral activation of ganciclovir (GCV) following transduction of tumor cells by retroviral vectors bearing the thymidine kinase (tk) gene has produced dramatic remissions of malignant gliomas in animal models. In human trials, although the technique has been deemed safe, little antitumor effect has been demonstrated. To evaluate the basis of this inefficacy in human gliomas, the authors conducted a gene-marking trial involving neuropathological and biochemical studies of treated tumor specimens.Methods. Five patients with malignant recurrent gliomas underwent stereotactic biopsy sampling and intratumoral implantation procedures with three aliquots of 106 vector-producing cells (VPCs) in columns. After 5 days, the tumor was resected and the tumor bed reimplanted with VPCs, and a course of GCV was given. Patients received clinical and radiological follow up for 6 months. Tumor specimens were analyzed neuropathologically and for tk gene expression by anti-TK immunohistochemistry and TK enzymatic activity.Four patients tolerated the treatment well but experienced tumor progression. The other developed an abscess after the second operation and died. Increased TK enzymatic activity was demonstrated in the one tumor specimen analyzed. Immunohistochemical evidence of tk gene expression was limited to VPCs. Transduction of tumor cells was not seen. Viable tumor cells were seen near VPCs containing TK. The lymphocytic immune response was mild.Conclusions. Except for the risk of infection inherent in reoperation, this tk—GCV paradigm was both feasible and safe. Pathological studies indicated that limited dissemination of VPCs and vector from the infusion site and failure to transduce tumor cells with the tk gene are major barriers to efficacy.

The role of CTCF in coordinating the expression of single gene loci

2011 ◽  
Vol 89 (5) ◽  
pp. 489-494 ◽  
Author(s):  
Austin E Gillen ◽  
Ann Harris
Keyword(s):  
Gene Expression ◽  
Mhc Class Ii ◽  
Noncoding Rna ◽  
Single Gene ◽  
Functional Model ◽  
Gene Clusters ◽  
Ctcf Binding ◽  
Chromatin Interactions ◽  
Insulator Elements

The CCCTC-binding factor (CTCF), which binds insulator elements in vertebrates, also facilitates coordinated gene expression at several gene clusters, including the β-globin, Igf2/H19 (insulin like growth factor 2/H19 noncoding RNA), and major histocompatibility complex (MHC) class II loci. CTCF controls expression of these genes both by enabling insulator function and facilitating higher order chromatin interactions. While the role of CTCF in gene regulation is best studied at these multi-gene loci, there is also evidence that CTCF contributes to the regulated expression of single genes. Here, we discuss how CTCF participates in coordinating gene expression at the CFTR (cystic fibrosis transmembrane conductance regulator) and IFNG (interferon-gamma) loci. We consider the structural similarities between the loci with regard to CTCF-binding elements, the possible interaction between nuclear receptors and CTCF, and the role of CTCF in chromatin looping at these genes. These comparisons reveal a functional model that may be applicable to other single-gene loci that require CTCF for coordinated gene expression.

scholarly journals Transcription of the Subtilase Cytotoxin Gene subAB1 in Shiga Toxin-Producing Escherichia coli Is Dependent on hfq and hns

2019 ◽  
Vol 85 (20) ◽  
Author(s):  
Laura Heinisch ◽  
Katharina Zoric ◽  
Maike Krause ◽  
Herbert Schmidt
Keyword(s):  
Gene Expression ◽  
Escherichia Coli ◽  
Shiga Toxin ◽  
Promoter Activity ◽  
Deletion Mutants ◽  
Content Type ◽  
E Coli ◽  
Intensive Investigation ◽  
Subtilase Cytotoxin

ABSTRACT Certain foodborne Shiga toxin-producing Escherichia coli (STEC) strains carry genes encoding the subtilase cytotoxin (SubAB). Although the mode of action of SubAB is under intensive investigation, information about the regulation of subAB gene expression is currently not available. In this study, we investigated the regulation of the chromosomal subAB1 gene in laboratory E. coli strain DH5α and STEC O113:H21 strain TS18/08 using a luciferase reporter gene assay. Special emphasis was given to the role of the global regulatory protein genes hfq and hns in subAB1 promoter activity. Subsequently, quantitative real-time PCR was performed to analyze the expression of Shiga toxin 2a (Stx2a), SubAB1, and cytolethal distending toxin V (Cdt-V) genes in STEC strain TS18/08 and its isogenic hfq and hns deletion mutants. The deletion of hfq led to a significant increase of up to 2-fold in subAB1 expression, especially in the late growth phase, in both strains. However, deletion of hns showed different effects on the promoter activity during the early and late exponential growth phases in both strains. Furthermore, upregulation of stx2a and cdt-V was demonstrated in hfq and hns deletion mutants in TS18/08. These data showed that the expression of subAB1, stx2a, and cdt-V is integrated in the regulatory network of global regulators Hfq and H-NS in Escherichia coli. IMPORTANCE Shiga toxin-producing Escherichia coli (STEC) strains are responsible for outbreaks of foodborne diseases, such as hemorrhagic colitis and the hemolytic uremic syndrome. The pathogenicity of those strains can be attributed to, among other factors, the production of toxins. Recently, the subtilase cytotoxin was detected in locus of enterocyte effacement (LEE)-negative STEC, and it was confirmed that it contributes to the cytotoxicity of those STEC strains. Although the mode of action of SubAB1 is under intensive investigation, the regulation of gene expression is currently not known. The global regulatory proteins H-NS and Hfq have impact on many cellular processes and have been described to regulate virulence factors as well. Here, we investigate the role of hns and hfq in expression of subAB1 as well as stx2a and cdt-V in an E. coli laboratory strain as well as in wild-type STEC strain TS18/08.

scholarly journals Genome Sequence and Biochemical Properties of Bifidobacterium longum Strain ICIS-505, Isolated from the Intestine of a Healthy Woman

2019 ◽  
Vol 8 (33) ◽  
Author(s):  
Sergey V. Andryuschenko ◽  
Elena V. Ivanova ◽  
Natalia B. Perunova ◽  
Oleg V. Bukharin
Keyword(s):  
Genome Sequence ◽  
Noncoding Rna ◽  
Bifidobacterium Longum ◽  
Healthy Woman ◽  
Biochemical Properties ◽  
Rrna Genes ◽  
Trna Genes ◽  
Human Feces ◽  
Content Type ◽  
Rna Genes

This report describes the genome sequence of Bifidobacterium longum strain ICIS-505, isolated from human feces. The size of the genome was 2,448,844 bp (59.71% G+C content), including 3,751 bp of the crypto-plasmid pBL505. Annotation revealed 2,241 gene sequences, including 2,033 proteins, 7 rRNA genes, 76 tRNA genes, and 4 noncoding RNA genes.

scholarly journals AB5Preassembly Is Not Required for Shiga Toxin Activity

2016 ◽  
Vol 198 (11) ◽  
pp. 1621-1630 ◽  
Author(s):  
Christine A. Pellino ◽  
Sayali S. Karve ◽  
Suman Pradhan ◽  
Alison A. Weiss
Keyword(s):  
Escherichia Coli ◽  
Enzymatic Activity ◽  
Hemolytic Uremic Syndrome ◽  
Shiga Toxin ◽  
Target Cells ◽  
Content Type ◽  
B Subunit ◽  
Uremic Syndrome ◽  
A Subunit ◽  
B Subunits

ABSTRACTShiga toxin (Stx)-producingEscherichia coli(STEC) is a major cause of foodborne illness, including the life-threatening complication hemolytic-uremic syndrome. The German outbreak in 2011 resulted in nearly 4,000 cases of infection, with 54 deaths. Two forms of Stx, Stx1 and Stx2, differ in potency, and subtype Stx2a is most commonly associated with fatal human disease. Stx is considered to be an AB5toxin. The single A (enzymatically active) subunit inhibits protein synthesis by cleaving a catalytic adenine from the eukaryotic rRNA. The B (binding) subunit forms a homopentamer and mediates cellular association and toxin internalization by binding to the glycolipid globotriaosylceramide (Gb3). Both subunits are essential for toxicity. Here we report that unlike other AB5toxin family members, Stx is produced by STEC as unassembled A and B subunits. A preformed AB5complex is not required for cellular toxicity orin vivotoxicity to mice, and toxin assembly likely occurs at the cell membrane. We demonstrate that disruption of A- and B-subunit association by use of A-subunit peptides that lack enzymatic activity can protect mice from lethal doses of toxin. Currently, no treatments have been proven to be effective for hemolytic-uremic syndrome. Our studies demonstrate that agents that interfere with A- and B-subunit assembly may have therapeutic potential. Shiga toxin (Stx) produced by pathogenicEscherichia coliis considered to be an AB5heterohexamer; however, no known mechanisms ensure AB5assembly. Stx released byE. coliis not in the AB5conformation and assembles at the receptor interface. Thus, unassembled Stx can impart toxicity. This finding shows that preventing AB5assembly is a potential treatment for Stx-associated illnesses.IMPORTANCEComplications due to Shiga toxin are frequently fatal, and at present, supportive care is the only treatment option. Furthermore, antibiotic treatment is contraindicated due to the ability of antibiotics to amplify bacterial expression of Shiga toxin. We report, contrary to prevailing assumptions, that Shiga toxin produced by STEC circulates as unassembled A and B subunits at concentrations that are lethal to mice. Similar to the case for anthrax toxin, assembly occurs on receptors expressed on the surfaces of mammalian target cells. Disruption of Shiga toxin assembly by use of A-subunit peptides that lack enzymatic activity protects mice from lethal challenge with Shiga toxin, suggesting a new approach for development of therapeutics.

scholarly journals Unprecedented High-Resolution View of Bacterial Operon Architecture Revealed by RNA Sequencing

mBio ◽  
2014 ◽  
Vol 5 (4) ◽  
Author(s):  
Tyrrell Conway ◽  
James P. Creecy ◽  
Scott M. Maddox ◽  
Joe E. Grissom ◽  
Trevor L. Conkle ◽  
...  
Keyword(s):  
Gene Expression ◽  
High Resolution ◽  
Rna Sequencing ◽  
Fine Tuning ◽  
Logarithmic Phase ◽  
Antisense Transcripts ◽  
Single Nucleotide ◽  
Content Type ◽  
E Coli ◽  
K 12

ABSTRACTWe analyzed the transcriptome ofEscherichia coliK-12 by strand-specific RNA sequencing at single-nucleotide resolution during steady-state (logarithmic-phase) growth and upon entry into stationary phase in glucose minimal medium. To generate high-resolution transcriptome maps, we developed an organizational schema which showed that in practice only three features are required to define operon architecture: the promoter, terminator, and deep RNA sequence read coverage. We precisely annotated 2,122 promoters and 1,774 terminators, defining 1,510 operons with an average of 1.98 genes per operon. Our analyses revealed an unprecedented view ofE. colioperon architecture. A large proportion (36%) of operons are complex with internal promoters or terminators that generate multiple transcription units. For 43% of operons, we observed differential expression of polycistronic genes, despite being in the same operons, indicating thatE. colioperon architecture allows fine-tuning of gene expression. We found that 276 of 370 convergent operons terminate inefficiently, generating complementary 3′ transcript ends which overlap on average by 286 nucleotides, and 136 of 388 divergent operons have promoters arranged such that their 5′ ends overlap on average by 168 nucleotides. We found 89 antisense transcripts of 397-nucleotide average length, 7 unannotated transcripts within intergenic regions, and 18 sense transcripts that completely overlap operons on the opposite strand. Of 519 overlapping transcripts, 75% correspond to sequences that are highly conserved inE. coli(>50 genomes). Our data extend recent studies showing unexpected transcriptome complexity in several bacteria and suggest that antisense RNA regulation is widespread.IMPORTANCEWe precisely mapped the 5′ and 3′ ends of RNA transcripts across theE. coliK-12 genome by using a single-nucleotide analytical approach. Our resulting high-resolution transcriptome maps show that ca. one-third ofE. colioperons are complex, with internal promoters and terminators generating multiple transcription units and allowing differential gene expression within these operons. We discovered extensive antisense transcription that results from more than 500 operons, which fully overlap or extensively overlap adjacent divergent or convergent operons. The genomic regions corresponding to these antisense transcripts are highly conserved inE. coli(includingShigellaspecies), although it remains to be proven whether or not they are functional. Our observations of features unearthed by single-nucleotide transcriptome mapping suggest that deeper layers of transcriptional regulation in bacteria are likely to be revealed in the future.

scholarly journals Comparative Analysis of Denitrifying Activities of Hyphomicrobium nitrativorans, Hyphomicrobium denitrificans, and Hyphomicrobium zavarzinii

2015 ◽  
Vol 81 (15) ◽  
pp. 5003-5014 ◽  
Author(s):  
Christine Martineau ◽  
Florian Mauffrey ◽  
Richard Villemur
Keyword(s):  
Gene Expression ◽  
Nitrate Reductase ◽  
Gene Clusters ◽  
Whole Genome Sequence ◽  
Nitrite Accumulation ◽  
Content Type ◽  
Denitrification Gene ◽  
Pure Cultures ◽  
Genetic Level ◽  
Membrane Bound

ABSTRACTHyphomicrobiumspp. are commonly identified as major players in denitrification systems supplied with methanol as a carbon source. However, denitrifyingHyphomicrobiumspecies are poorly characterized, and very few studies have provided information on the genetic and physiological aspects of denitrification in pure cultures of these bacteria. This is a comparative study of three denitrifyingHyphomicrobiumspecies,H. denitrificansATCC 51888,H. zavarziniiZV622, and a newly described species,H. nitrativoransNL23, which was isolated from a denitrification system treating seawater. Whole-genome sequence analyses revealed that although they share numerous orthologous genes, these three species differ greatly in their nitrate reductases, with gene clusters encoding a periplasmic nitrate reductase (Nap) inH. nitrativorans, a membrane-bound nitrate reductase (Nar) inH. denitrificans, and one Nap and two Nar enzymes inH. zavarzinii. Concurrently with these differences observed at the genetic level, important differences in the denitrification capacities of theseHyphomicrobiumspecies were determined.H. nitrativoransgrew and denitrified at higher nitrate and NaCl concentrations than did the two other species, without significant nitrite accumulation. Significant increases in the relative gene expression levels of the nitrate (napA) and nitrite (nirK) reductase genes were also noted forH. nitrativoransat higher nitrate and NaCl concentrations. Oxygen was also found to be a strong regulator of denitrification gene expression in bothH. nitrativoransandH. zavarzinii, although individual genes responded differently in these two species. Taken together, the results presented in this study highlight the potential ofH. nitrativoransas an efficient and adaptable bacterium that is able to perform complete denitrification under various conditions.

scholarly journals Draft Genome Sequence of Bacillus thuringiensis Strain UNMSM10RA, Isolated from Potato Crop Soil in Peru

2020 ◽  
Vol 9 (2) ◽  
Author(s):  
Yolanda Bedsabé Delgado-Silva ◽  
David Tarazona ◽  
Fernando Serna ◽  
Eduardo Juscamayta ◽  
Julio César Chávez-Galarza ◽  
...  
Keyword(s):  
Bacillus Thuringiensis ◽  
Genome Sequence ◽  
Noncoding Rna ◽  
Potato Crop ◽  
Draft Genome ◽  
Rrna Genes ◽  
Trna Genes ◽  
Protein Coding ◽  
Coding Sequences ◽  
Content Type

The 5.5-Mb genome sequence of Bacillus thuringiensis strain UNMSM10RA, isolated from potato crop soil, is reported in this study. The strain UNMSM10RA contains 5,347 protein-coding sequences, 105 tRNA genes, 15 rRNA genes, and 5 noncoding RNA (ncRNA) genes, with an average G+C content of 35.1%.

scholarly journals MUNC, a Long Noncoding RNA That Facilitates the Function of MyoD in Skeletal Myogenesis

2014 ◽  
Vol 35 (3) ◽  
pp. 498-513 ◽  
Author(s):  
Adam C. Mueller ◽  
Magdalena A. Cichewicz ◽  
Bijan K. Dey ◽  
Ryan Layer ◽  
Brian J. Reon ◽  
...  
Keyword(s):  
Gene Expression ◽  
Noncoding Rna ◽  
Regulatory Region ◽  
Myoblast Differentiation ◽  
Content Type ◽  
Multiple Promoters ◽  
Enhancer Rna ◽  
Distal Regulatory Region ◽  
Interfering Rna

Anin silicoscreen for myogenic long noncoding RNAs (lncRNAs) revealed nine lncRNAs that are upregulated more than 10-fold in myotubes versus levels in myoblasts. One of these lncRNAs, MyoD upstream noncoding (MUNC, also known as DRReRNA), is encoded 5 kb upstream of the transcription start site ofMyoD, a myogenic transcription factor gene. MUNC is specifically expressed in skeletal muscle and exists as in unspliced and spliced isoforms, and its 5′ end overlaps with thecis-acting distal regulatory region (DRR) ofMyoD. Small interfering RNA (siRNA) of MUNC reduced myoblast differentiation and specifically reduced the association of MyoD to the DRR enhancer and myogenin promoter but not to another MyoD-dependent enhancer. Stable overexpression of MUNC from a heterologous promoter increased endogenousMyoD,Myogenin, andMyh3(myosin heavy chain, [MHC] gene) mRNAs but not the cognate proteins, suggesting that MUNC can act intransto promote gene expression but that this activity does not require an induction of MyoD protein. MUNC also stimulates the transcription of other genes that are not recognized as MyoD-inducible genes. Knockdown of MUNCin vivoimpaired murine muscle regeneration, implicating MUNC in primary satellite cell differentiation in the animal. We also discovered a human MUNC that is induced during differentiation of myoblasts and whose knockdown decreases differentiation, suggesting an evolutionarily conserved role of MUNC lncRNA in myogenesis. Although MUNC overlaps with the DRR enhancer, our results suggest that MUNC is not a classiccis-acting enhancer RNA (e-RNA) acting exclusively by stimulating the neighboringMyoDgene but more like a promyogenic lncRNA that acts directly or indirectly on multiple promoters to increase myogenic gene expression.

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