scholarly journals RNA-mediated interaction of Cajal bodies and U2 snRNA genes

2001 ◽  
Vol 154 (3) ◽  
pp. 499-510 ◽  
Author(s):  
Mark R. Frey ◽  
A. Gregory Matera
Keyword(s):  
Nuclear Export ◽  
Marked Decrease ◽  
Gene Clusters ◽  
Cajal Bodies ◽  
U2 Snrna ◽  
Intragenic Deletions ◽  
High Concentrations ◽  
Nuclear Structures ◽  
Insight Into ◽  
Small Nuclear Ribonucleoproteins

Cajal bodies (CBs) are nuclear structures involved in RNA metabolism that accumulate high concentrations of small nuclear ribonucleoproteins (snRNPs). Notably, CBs preferentially associate with specific genomic loci in interphase human cells, including several snRNA and histone gene clusters. To uncover functional elements involved in the interaction of genes and CBs, we analyzed the expression and subcellular localization of stably transfected artificial arrays of U2 snRNA genes. Although promoter substitution arrays colocalized with CBs, constructs containing intragenic deletions did not. Additional experiments identified factors within CBs that are important for association with the native U2 genes. Inhibition of nuclear export or targeted degradation of U2 snRNPs caused a marked decrease in the levels of U2 snRNA in CBs and strongly disrupted the interaction with U2 genes. Together, the results illustrate a specific requirement for both the snRNA transcripts as well as the presence of snRNPs (or snRNP proteins) within CBs. Our data thus provide significant insight into the mechanism of CB interaction with snRNA loci, strengthening the putative role for this nuclear suborganelle in snRNP biogenesis.

scholarly journals Coiled Bodies and U2 snRNA Genes Adjacent to Coiled Bodies Are Enriched in Factors Required for snRNA Transcription

1998 ◽  
Vol 9 (5) ◽  
pp. 1025-1036 ◽  
Author(s):  
Wouter Schul ◽  
Roel van Driel ◽  
Luitzen de Jong
Keyword(s):  
Transcription Factor ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Gene Clusters ◽  
Small Nuclear Rna ◽  
U2 Snrna ◽  
Coiled Bodies ◽  
High Concentrations ◽  
Tata Box Binding Protein ◽  
Nuclear Domains

A significant percentage of the gene clusters that contain the human genes for U1 small nuclear RNA (snRNA) or for U2 snRNA have been found associated with small nuclear domains, known as coiled bodies. We show here, by immunofluorescent labeling of human cells, that coiled bodies are enriched in factors required for the transcription of these snRNA genes. The 45-kDa γ-subunit of the transcription factor, proximal element sequence-binding transcription factor (PTF), which is specific for the snRNA genes, was found in high concentrations in coiled bodies, along with the general transcription factor TATA-box binding protein and a subset of RNA polymerase II. We show that the transcription factors and RNA polymerase II are concentrated in irregularly shaped domains that not only overlap with coiled bodies but also extend to their immediate surroundings. Fluorescent in situ hybridization showed that these domains can overlap with U2 snRNA genes adjacent to coiled bodies. In addition, we found the domains to contain newly synthesized RNA, visualized by 5-bromo-uridine triphosphate labeling. Our data suggest that coiled bodies are involved in the expression of snRNA genes, which leads us to propose the model that coiled bodies are associated with snRNA genes to facilitate and regulate their transcription. These findings point to a general principle of higher order organization of gene expression in the nucleus.

Phylogeny of actin and tubulin gene homologs in diverse eukaryotic species

2019 ◽  
Vol 79 (01S) ◽  
Author(s):  
Pawan Kumar Jayaswal ◽  
Asheesh Shanker ◽  
Nagendra Kumar Singh
Keyword(s):  
Evolutionary Relationship ◽  
Genomic Data ◽  
Gene Clusters ◽  
Species Trees ◽  
Model Species ◽  
Tubulin Gene ◽  
Tubulin Genes ◽  
Eukaryotic Species ◽  
Relationship Of ◽  
Insight Into

Actin and tubulin are cytoskeleton proteins, which are important components of the celland are conserved across species. Despite their crucial significance in cell motility and cell division the distribution and phylogeny of actin and tubulin genes across taxa is poorly understood. Here we used publicly available genomic data of 49 model species of plants, animals, fungi and Protista for further understanding the distribution of these genes among diverse eukaryotic species using rice as reference. The highest numbers of rice actin and tubulin gene homologs were present in plants followed by animals, fungi and Protista species, whereas ten actin and nine tubulin genes were conserved in all 49 species. Phylogenetic analysis of 19 actin and 18 tubulin genes clustered them into four major groups each. One each of the actin and tubulin gene clusters was conserved across eukaryotic species. Species trees based on the conserved actin and tubulin genes showed evolutionary relationship of 49 different taxa clustered into plants, animals, fungi and Protista. This study provides a phylogenetic insight into the evolution of actin and tubulin genes in diverse eukaryotic species.

Hepatic uptake of intact glutathione S-conjugate, inhibition by organic anions, and sinusoidal catabolism

1993 ◽  
Vol 265 (3) ◽  
pp. G547-G554
Author(s):  
C. A. Hinchman ◽  
A. T. Truong ◽  
N. Ballatori
Keyword(s):  
Guinea Pig ◽  
Rat Liver ◽  
Marked Decrease ◽  
Hepatic Uptake ◽  
Half Time ◽  
High Concentrations ◽  
Rat Livers ◽  
Dose Dependent ◽  
Uptake And Metabolism ◽  
Guinea Pig Liver

To identify potential mechanisms for hepatic removal of circulating glutathione (GSH) conjugates, uptake and metabolism of S-2,4-dinitrophenylglutathione (DNP-SG) were examined in isolated perfused livers from rat and guinea pig. Guinea pig livers perfused with 5 mumol of DNP-SG in a recirculating system (50 microM initial concn) rapidly cleared the conjugate from the perfusate (half time 3.7 min), whereas clearance was considerably slower in rat liver (half time 35 min). Disappearance of DNP-SG from the perfusate was accompanied by a simultaneous appearance of DNP-SG and its metabolites in bile. Addition of acivicin, an inhibitor of gamma-glutamyltransferase (gamma-GT), to the perfusate resulted in a marked decrease in DNP-SG clearance by guinea pig liver but had no effect in rat liver, suggesting that in the guinea pig this process is largely dependent on sinusoidal gamma-GT activity. However, even in the presence of acivicin, rat and guinea pig livers removed nearly one-half of the administered DNP-SG from the recirculating perfusate over 30 min. High concentrations of DNP-SG were found in bile (up to 3.7 mM), indicating that the liver is capable of transporting the intact conjugate from the circulation. When rat livers were perfused with higher concentrations of DNP-SG (100 and 250 microM), biliary excretion of DNP-SG increased dose dependently, with concentrations in bile reaching 10 mM at the higher dose. This was accompanied by a dose-dependent choleresis.(ABSTRACT TRUNCATED AT 250 WORDS)

scholarly journals Dynamic Nature of Cleavage Bodies and Their Spatial Relationship to DDX1 Bodies, Cajal Bodies, and Gems

2006 ◽  
Vol 17 (3) ◽  
pp. 1126-1140 ◽  
Author(s):  
Lei Li ◽  
Ken Roy ◽  
Sachin Katyal ◽  
Xuejun Sun ◽  
Stacey Bléoo ◽  
...  
Keyword(s):  
Rna Polymerase Ii ◽  
Actin Polymerization ◽  
Spatial Relationship ◽  
S Phase ◽  
Nuclear Bodies ◽  
Cajal Bodies ◽  
Rna Transcription ◽  
Nuclear Structures ◽  
The Relationship ◽  
Striking Effect

DDX1 bodies, cleavage bodies, Cajal bodies (CBs), and gems are nuclear suborganelles that contain factors involved in RNA transcription and/or processing. Although all four nuclear bodies can exist as distinct entities, they often colocalize or overlap with each other. To better understand the relationship between these four nuclear bodies, we examined their spatial distribution as a function of the cell cycle. Here, we report that whereas DDX1 bodies, CBs and gems are present throughout interphase, CPSF-100-containing cleavage bodies are predominantly found during S and G2 phases, whereas CstF-64-containing cleavage bodies are primarily observed during S phase. All four nuclear bodies associate with each other during S phase, with cleavage bodies colocalizing with DDX1 bodies, and cleavage bodies/DDX1 bodies residing adjacent to gems and CBs. Although inhibitors of RNA transcription had no effect on DDX1 bodies or cleavage bodies, inhibitors of DNA replication resulted in loss of CstF-64-containing cleavage bodies. A striking effect on nuclear structures was observed with latrunculin B, an inhibitor of actin polymerization, resulting in the formation of needlelike nuclear spicules made up of CstF-64, CPSF-100, RNA, and RNA polymerase II. Our results suggest that cleavage body components are highly dynamic in nature.

Characterization of nuclear structures containing superhelical DNA

1976 ◽  
Vol 22 (2) ◽  
pp. 303-324 ◽  
Author(s):  
P.R. Cook ◽  
I.A. Brazell ◽  
E. Jost
Keyword(s):  
Protein Content ◽  
Ionic Detergents ◽  
High Concentrations ◽  
Nuclear Structures ◽  
Intercalating Agents ◽  
Made In

Structures resembling nuclei but depleted of protein may be released by gently lysing cells in solutions containing non-ionic detergents and high concentrations of salt. These nucleoids sediment in gradients containing intercalating agents in a manner characteristic of DNA that is intact, supercoiled and circular. The concentration of salt present during isolation of human nucleoids affects their protein content. When made in I-95 M NaCl they lack histones and most of the proteins characteristic of chromatin; in 1-0 M NaCl they contain variable amounts of histones. The effects of various treatments on nucleoid integrity were investigated.

scholarly journals Synthesis of Platinum Nanocrystals within Iodine Ions Mediated

2018 ◽  
Vol 2018 ◽  
pp. 1-10 ◽  
Author(s):  
Jiamao Li ◽  
Jingwei Hou ◽  
Yu Gong ◽  
Chengjian Xiao ◽  
Lei Yue ◽  
...  
Keyword(s):  
Shape Control ◽  
Growth Process ◽  
Growth Stage ◽  
Nucleation Stage ◽  
Platinum Nanocrystals ◽  
High Resolution Tem ◽  
Pt Nanocrystals ◽  
High Concentrations ◽  
Insight Into

A liquid-phase reducing method of synthesizing Pt nanocrystals was demonstrated, and dendrite-, cube-, and cuboctahedron-shaped Pt nanocrystals (NCs) with well-defined monomorphic were successfully synthesized through iodine ions mediated with the CTAB agent. When the KI concentration was increased to thirty times of K2PtCl4 at the nucleation stage, the high-quality Pt nanodendrites could be obtained. However, no matter how many KI were added at the growth age, only cube- and cuboctahedron-shaped Pt nanocrystals formed. The results of high-resolution TEM, EDX, and XRD indicated that the size and shape of Pt NCs could be turned by changing the concentration and time of KI. In the nucleation stage, it might be due to that some iodine ions adsorb on the surfaces of Pt NCs, which probably cause the rapid growth process resulting in the formation of Pt nanodendrites. In the growth stage, although high concentrations of I− ions could contribute to the shape control and generate bigger particles of Pt NCs, small Pt particles do not grow into dendrites. The insight into the role of I− ions in synthesis of Pt NCs reported here provided a viewpoint for clearly understanding the formation mechanism of anisotropic platinum nanostructures.

scholarly journals Comparative genomics of biotechnologically important yeasts

2016 ◽  
Vol 113 (35) ◽  
pp. 9882-9887 ◽  
Author(s):  
Robert Riley ◽  
Sajeet Haridas ◽  
Kenneth H. Wolfe ◽  
Mariana R. Lopes ◽  
Chris Todd Hittinger ◽  
...  
Keyword(s):  
Gene Clusters ◽  
Xylose Utilization ◽  
Comparative Genome Analysis ◽  
Pachysolen Tannophilus ◽  
Biochemical Traits ◽  
Code Change ◽  
Mating Type Switching ◽  
Yeast Phylogeny ◽  
Genomic Basis ◽  
Insight Into

Ascomycete yeasts are metabolically diverse, with great potential for biotechnology. Here, we report the comparative genome analysis of 29 taxonomically and biotechnologically important yeasts, including 16 newly sequenced. We identify a genetic code change, CUG-Ala, in Pachysolen tannophilus in the clade sister to the known CUG-Ser clade. Our well-resolved yeast phylogeny shows that some traits, such as methylotrophy, are restricted to single clades, whereas others, such as l-rhamnose utilization, have patchy phylogenetic distributions. Gene clusters, with variable organization and distribution, encode many pathways of interest. Genomics can predict some biochemical traits precisely, but the genomic basis of others, such as xylose utilization, remains unresolved. Our data also provide insight into early evolution of ascomycetes. We document the loss of H3K9me2/3 heterochromatin, the origin of ascomycete mating-type switching, and panascomycete synteny at the MAT locus. These data and analyses will facilitate the engineering of efficient biosynthetic and degradative pathways and gateways for genomic manipulation.

scholarly journals Environmental Threats of Ancient Pb Mining and Metallurgical Activities in the Linares Mining District (Southern Spain)

Proceedings ◽  
2018 ◽  
Vol 2 (23) ◽  
pp. 1459
Author(s):  
Carlos Boente ◽  
Carlos Sierra ◽  
Julián Martínez ◽  
Eduardo Rodríguez-Valdés ◽  
Elías Afif ◽  
...  
Keyword(s):  
Risk Assessment ◽  
Toxic Elements ◽  
Potentially Toxic Elements ◽  
Mining District ◽  
Land Uses ◽  
Environmental Threats ◽  
Industrial Sites ◽  
High Concentrations ◽  
Insight Into ◽  
Metallurgical Activities

Former industrial sites are now dedicated to other land uses in the Linares mining district. Here we selected five residential/farming areas (squares of 1 km2 each) and sought to evaluate the levels of contamination by Potentially Toxic Elements (PTEs) of the soils, and also to offer an insight into the threat these pollutants may pose to human health or the environment by means of risk assessment. High concentrations especially of Pb, and also of As, Cd, Cu and Zn were found in quantities that are considerably bioavailable. Moreover, risk assessment revealed unacceptable concentrations for Pb and As in all the areas as well as for Cd and Cu in some squares.

RNA Splicing by the Spliceosome

2020 ◽  
Vol 89 (1) ◽  
pp. 359-388 ◽  
Author(s):  
Max E. Wilkinson ◽  
Clément Charenton ◽  
Kiyoshi Nagai
Keyword(s):  
Splice Site ◽  
Active Site ◽  
Rna Splicing ◽  
Messenger Rna ◽  
Structural Studies ◽  
U2 Snrna ◽  
U6 Snrna ◽  
Mature Mrna ◽  
Catalytic Metal ◽  
Small Nuclear Ribonucleoproteins

The spliceosome removes introns from messenger RNA precursors (pre-mRNA). Decades of biochemistry and genetics combined with recent structural studies of the spliceosome have produced a detailed view of the mechanism of splicing. In this review, we aim to make this mechanism understandable and provide several videos of the spliceosome in action to illustrate the intricate choreography of splicing. The U1 and U2 small nuclear ribonucleoproteins (snRNPs) mark an intron and recruit the U4/U6.U5 tri-snRNP. Transfer of the 5′ splice site (5′SS) from U1 to U6 snRNA triggers unwinding of U6 snRNA from U4 snRNA. U6 folds with U2 snRNA into an RNA-based active site that positions the 5′SS at two catalytic metal ions. The branch point (BP) adenosine attacks the 5′SS, producing a free 5′ exon. Removal of the BP adenosine from the active site allows the 3′SS to bind, so that the 5′ exon attacks the 3′SS to produce mature mRNA and an excised lariat intron.

scholarly journals Use of Permanent Wall-Deficient Cells as a System for the Discovery of New-to-Nature Metabolites

2020 ◽  
Vol 8 (12) ◽  
pp. 1897
Author(s):  
Shraddha Shitut ◽  
Güniz Özer Bergman ◽  
Alexander Kros ◽  
Daniel E. Rozen ◽  
Dennis Claessen
Keyword(s):  
Cell Wall ◽  
Secondary Metabolites ◽  
Gene Clusters ◽  
Chemical Diversity ◽  
Biosynthetic Gene Clusters ◽  
Microbial Cell Factories ◽  
Cell Factories ◽  
Genome Recombination ◽  
Antibiotic Discovery ◽  
Insight Into

Filamentous actinobacteria are widely used as microbial cell factories to produce valuable secondary metabolites, including the vast majority of clinically relevant antimicrobial compounds. Secondary metabolites are typically encoded by large biosynthetic gene clusters, which allow for a modular approach to generating diverse compounds through recombination. Protoplast fusion is a popular method for whole genome recombination that uses fusion of cells that are transiently wall-deficient. This process has been applied for both inter- and intraspecies recombination. An important limiting step in obtaining diverse recombinants from fused protoplasts is regeneration of the cell wall, because this forces the chromosomes from different parental lines to segregate, thereby preventing further recombination. Recently, several labs have gained insight into wall-deficient bacteria that have the ability to proliferate without their cell wall, known as L-forms. Unlike protoplasts, L-forms can stably maintain multiple chromosomes over many division cycles. Fusion of such L-forms would potentially allow cells to express genes from both parental genomes while also extending the time for recombination, both of which can contribute to an increased chemical diversity. Here, we present a perspective on how L-form fusion has the potential to become a platform for novel compound discovery and may thus help to overcome the antibiotic discovery void.

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