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Terminator Regions, Genetic (0):
Recent article
Terminator Regions, Genetic
Abstract
We developed novel promoter-probe and terminator-probe vectors based on the Streptococcus agalactiae pMV158 plasmid, which replicates autonomously in numerous Gram-positive bacteria. As reporter gene, a gfp allele encoding a variant of the green fluorescent protein was used. These genetic tools were...
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PMID: 20801171
PDF is available here.
PDF is available here.
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Abstract
We used budding yeast to identify the factors assisting fork fusion at replicating chromosomes. Using genomic and mechanistic studies, we have identified and characterized 71 chromosomal termination regions (TERs). TERs contain fork pausing elements that influence fork progression and merging. The R...
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PMID: 20797631
PDF is available here.
PDF is available here.
Abstract
We have solved the structure of a member of this family, the human mitochondrial transcriptional terminator MTERF1, bound to dsDNA containing the termination sequence. The structure indicates that upon sequence recognition MTERF1 unwinds the DNA molecule, promoting eversion of three nucleotides. Bas...
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PMID: 20550934
PDF is available here.
PDF is available here.
Abstract
We examined the effect of CREM siRNA on forskolin-stimulated ICER formation and CRH transcription in the hypothalamic cell line, 4B, and in primary cultures of hypothalamic neurons. Cotransfection of 4B cells with CREM siRNA and a CRH promoter-driven luciferase reporter gene markedly reduced the ind...
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PMID: 19543827
PDF is available here.
PDF is available here.
Hereditas (Beijing) (31)8 2009
Abstract
We obtained the P0 generation of "all fish" transgenic fish farming groups. Comparing the activities of the two different transgenic vectors, the weight distribution of the breeding groups from growth hormone gene terminator transgenic vector felt into a normal distribution; however, the weight dist...
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PMID: 19689944
PDF is available here.
PDF is available here.
Biochimica et Biophysica Acta (1789)9-10 2009
Abstract
Riboswitches are non-protein coding RNA elements typically found in the 5' untranslated region (5'-UTR) of mRNAs that utilize metabolite binding to control expression of their own transcript. The RNA-ligand interaction causes conformational changes in the RNA that direct the cotranscriptional folding...
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PMID: 19595806
PDF is available here.
PDF is available here.
Gene Therapy (16)7 2009
Abstract
We designed a lentiviral vector carrying two transcriptional units separated by polyadenylation, terminator and insulator sequences. With this design, the expression level of both genes was as high as that yielded from lentiviral vectors containing only a single transcriptional unit. Similar results...
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PMID: 19440229
PDF is available here.
PDF is available here.
Methods in Molecular Biology (554)554 2009
Abstract
We used such a system to investigate the transcription termination properties of the sea urchin factor mtDBP, however, it is applicable to the study of transcription termination in a variety of organisms, provided that the pure mtRNAP and the transcription termination factor are available.The assay...
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PMID: 19513672
PDF is available here.
PDF is available here.
Abstract
Abstract
Size matched fragments containing the polyadenylation signal of the human beta-actin gene (ACTB) and the human beta-globin gene (HBB) were evaluated for transcription termination using this new ratiometric tandem reporter assay. Constructs bearing just 200 base pairs on either side of the consensus...
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PMID: 19587781
PDF is available here.
PDF is available here.
Abstract
We describe the use of intragenic gene transfer technology towards disease resistance in potatoes. An expression cassette was constructed with the 5' promoter and 3' terminator regions of a potato gene encoding a chlorophyll a/b binding protein (StLhca3). The coding regions of the StSN1 and StSN2 ge...
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PMID: 20222549
PDF is available here.
PDF is available here.
Abstract
We show here that altering the distance between these two loops suggests that G7, A8, and A9 from the internal loop and A19 and G20 from the hairpin loop constitute two structurally discrete TRAP-binding regions. Photochemical cross-linking experiments also show that the hairpin loop of the 5'SL is...
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PMID: 19033375
PDF is available here.
PDF is available here.
Abstract
We found the covR/S operon produced three RNA transcripts (around 2.5-, 1.0-, and 0.8-kb in size). Using RNA transcriptional terminator sequence prediction and transcriptional terminator analysis, we identified two atypical rho-independent terminator sequences downstream of the covR gene and showed...
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PMID: 18824088
PDF is available here.
PDF is available here.
Molecular Cell (32)6 2008
Transcription by moonlight: structural basis of an extraribosomal activity of ribosomal protein S10.
Abstract
In this issue of Molecular Cell, Luo et al. (2008) show that S10 protein can function in the ribosome or the transcript elongation complex with minimal structural change, providing new insights into the roles of S10 and NusB in transcript elongation.
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PMID: 19111651
PDF is available here.
PDF is available here.
Molecular Cell (32)6 2008
Abstract
We used complementation assays and recombineering to delineate regions of S10 dispensable for antitermination, and determined the crystal structure of a transcriptionally active NusB-S10 complex. In this complex, S10 adopts the same fold as in the 30S subunit and is blocked from simultaneous associa...
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PMID: 19111659
PDF is available here.
PDF is available here.
Methods in Molecular Biology (502)502 2008
Abstract
Knowledge of the regulatory elements contained within bacteriophage genomes forms the basis for understanding genomic expression and organization. The in silico prediction of promoter and terminator sequences in phage genomes is a first step towards this understanding. In this chapter, a number of p...
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PMID: 19082554
PDF is available here.
PDF is available here.
Abstract
We developed a stochastic model, integrating results of single-molecule and quantitative in vivo studies of Escherichia coli, to evaluate the quantitative effect of pausing, termination, and antitermination (AT) on rRNA transcription. Our calculations reveal that in dense RNAP traffic, spontaneous p...
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PMID: 19017803
PDF is available here.
PDF is available here.
Abstract
We identify suppressors encoding proteins that play roles in processes at the 3′ ends of genes by exploiting a mutation in which the 3′ end of another gene is transposed into the first gene of the operon. As expected, genes encoding CPSF and CstF were identified in the screen. We also report th...
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PMID: 18946043
PDF is available here.
PDF is available here.
Journal of Bacteriology (190)21 2008
Abstract
We tested putative rrn transcription antitermination-inducing sequences from five different bacteria for their abilities to function in E. coli. We further examined their response to the lack of one known rrn transcription antitermination protein from E. coli, NusB. We monitored antitermination acti...
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PMID: 18757535
PDF is available here.
PDF is available here.
Abstract
In this work, it was discovered that the stability of mRNA in a cell-free extract could be controlled by using engineered T7 terminator sequences. Specifically, it was found that mRNA stability gradually decreased as the length of the stem structure of the T7 terminator was reduced sequentially. As...
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PMID: 18404770
PDF is available here.
PDF is available here.
Abstract
I antifreeze protein analogue (rAFP) in L. lactis was optimized. An efficient SlpA promoter (P SlpA) was fused to various signal peptides (SPs) and propeptide sequences to examine the extracellular expression levels of rAFP. An efficient signal peptide, SP sacB, fused to prosequence AE, enabled high...
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PMID: 18759446
PDF is available here.
PDF is available here.
Journal of Molecular Biology (381)5 2008
Abstract
We examined several bacterial genomes for tRNA genes where the expression might be potentially affected by structural elements located outside of the mature tRNA. In Pseudomonas aeruginosa, our analysis suggested that the tRNA(Trp) is transcribed together with a putative stem-loop structure followed...
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PMID: 18625241
PDF is available here.
PDF is available here.
Molecular Cell (31)5 2008
Abstract
We describe here a nonconventional mechanism of transcriptional regulation that relies on the selection of alternative transcription start sites to generate CUTs or mRNAs. Transcription from TATA box proximal start sites generates unstable transcripts and downregulates expression of the URA2 gene un...
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PMID: 18775327
PDF is available here.
PDF is available here.
Molecular Cell (31)5 2008
Abstract
Recent work from Kuehner and Brow (2008) and Thiebaut et al. (2008) in Molecular Cell and Jenks et al. (2008) in Molecular and Cellular Biology reveals that regulated expression of central nucleotide synthesis pathway components directs start site-dependent RNA polymerase II termination.
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PMID: 18775320
PDF is available here.
PDF is available here.
Journal of Molecular Biology (380)5 2008
Abstract
The Nun protein of coliphage HK022 excludes superinfecting lambda phage. Nun recognizes and binds to the N utilization (nut) sites on phage lambda nascent RNA and induces transcription termination. Overexpression of Nun from a high-copy plasmid is toxic for Escherichia coli, despite the fact that nu...
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PMID: 18571198
PDF is available here.
PDF is available here.
Journal of Biological Chemistry (283)29 2008
Abstract
We hypothesized that the conformational state(s) of the EC associated with this pausing would influence the action of Rho. Analyses of the pausing behavior of the EC at the termination points of two well known Rho-dependent terminators revealed that Rho prefers actively transcribing complexes for te...
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PMID: 18482981
PDF is available here.
PDF is available here.
Abstract
I and either ATP or dATP. This argues for a two step model: the specifying step, requiring both VTF and UUUUUNU, and the energy-dependent step employing NPH I and ATP. Evaluation of NPH I mutants for the ability to stimulate transcription elongation demonstrated that ATPase activity and a stable int...
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PMID: 18433825
PDF is available here.
PDF is available here.
Abstract
These results support a model in which the availability of the UUUUUNU motif outside of the transcribing RNA polymerase permits binding of both transcription termination factors, VTF and Rap94, to UUUUUNU. The assembly of this termination complex initiates the transcription termination sequence....
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PMID: 18455214
PDF is available here.
PDF is available here.
Abstract
The T box transcription antitermination system is a riboswitch found primarily in Gram-positive bacteria which monitors the aminoacylation of the cognate tRNA and regulates a variety of amino acid-related genes. Novel 4,5-disubstituted oxazolidinones were identified as high affinity RNA molecular ef...
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PMID: 18502126
PDF is available here.
PDF is available here.
Characterizing riboswitch function: identification of Mg2+ binding site in T box antiterminator RNA.
Abstract
T box bacterial genes utilize a riboswitch mechanism to regulate gene expression at the transcriptional level. Complementary base pairing of the 5'-untranslated mRNA with uncharged cognate tRNA stabilizes formation of an antiterminator element and permits complete transcription. In the absence of tR...
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PMID: 18371302
PDF is available here.
PDF is available here.
Cancer Gene Therapy (15)5 2008
Abstract
We constructed a conditionally replication-competent adenovirus in which expression of the adenoviral E1A gene, necessary for replication, is driven by the cancer-specific promoter of progression-elevated gene-3 (PEG-3) and which simultaneously expresses mda-7/IL-24 in the E3 region of the adenoviru...
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PMID: 18323853
PDF is available here.
PDF is available here.
EMBO Journal (27)8 2008
Abstract
We show epigenetic and spatial organization of mouse rRNA genes at the molecular level. TTF-I-binding sites subdivide the rRNA transcription unit into functional chromatin domains and sharply delimit transcription factor occupancy. H2A.Z-containing nucleosomes occupy the spacer promoter next to a ne...
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PMID: 18354495
PDF is available here.
PDF is available here.
Genes & Development (22)8 2008
Abstract
We report that the activity of Rat1 is also required for efficient termination by RNA polymerase I (Pol I) on the rDNA. In strains lacking catalytically active Rat1 or its cofactor Rai1, Pol I reads through the major, "Reb1-dependent" terminator (T1) but stops downstream at the "fail-safe" terminato...
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PMID: 18413717
PDF is available here.
PDF is available here.
Genes & Development (22)8 2008
Abstract
We demonstrate that both Rat1p exonuclease and Sen1p helicase are required for efficient termination by promoting degradation of the nascent transcript associated with Pol II, following mRNA 3' end processing. Similarly, Pol I termination relies on prior Rnt1p cleavage at the 3' end of the pre-rRNA...
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PMID: 18413718
PDF is available here.
PDF is available here.
Abstract
We demonstrate by gene conformation analysis in both human cell lines and mouse mammary tissue that gene loops are imposed on BRCA1 between the promoter, introns, and terminator region. Significantly, association between the BRCA1 promoter and terminator regions change upon estrogen stimulation and...
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PMID: 18375767
PDF is available here.
PDF is available here.
Abstract
In this issue, Larson et al. (2008) describe the use of optical traps to pull on the DNA template or RNA transcript and thereby explore the termination mechanism for E. coli RNA polymerase at intrinsic terminators. Their results imply that, depending on the nature of the terminator sequence, RNA pol...
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PMID: 18358802
PDF is available here.
PDF is available here.
Abstract
We used single-molecule techniques to investigate the mechanism by which three representative terminators (his, t500, and tR2) destabilize the elongation complex (EC). For his and tR2 terminators, loads exerted to bias translocation did not affect termination efficiency (TE). However, the force-depe...
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PMID: 18358810
PDF is available here.
PDF is available here.
Abstract
We cloned the plg1 (pectin lyase 1) from Penicillium griseoroseum gene under the control of the strong constitutive promoter of the glyceraldehyde-3-phosphate dehydrogenase gene (gpdA) and the terminator region of the tryptophan synthetase (trpC) gene from Aspergillus nidulans (plasmid pAN52-Plg1) a...
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PMID: 18030511
PDF is available here.
PDF is available here.
Journal of Molecular Biology (376)3 2008
Abstract
We have determined the structure of NusB from the thermophilic bacterium Aquifex aeolicus and studied the interaction of NusB and NusE. We characterize this binding interaction using NMR, isothermal titration calorimetry, gel filtration, and analytical ultracentrifugation. The binding site of NusE o...
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PMID: 18177898
PDF is available here.
PDF is available here.
Journal of Molecular Biology (376)2 2008
Abstract
We use solution and RNAP-tethered chemical nucleases to probe the CJ transcript and changes in the EC structure as the polymerase pauses and terminates at the CJ. Together with extensive mutational scanning of regions of the polymerase that are likely to be involved in recognition of the CJ, we are...
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PMID: 18166198
PDF is available here.
PDF is available here.
Abstract
Changes in near UV circular dichroism (CD) and fluorescence spectra of site-specifically placed pairs of 2-aminopurine residues have been used to probe the roles of the RNA hairpin and the RNA-DNA hybrid in controlling intrinsic termination of transcription. Functional transcription complexes were a...
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PMID: 18070878
PDF is available here.
PDF is available here.
Abstract
We were able to locate turning points on the Mycoplasma genomes, with the minimum and maximum points co-locating with ori or ter in the reference genomes. Assuming Z curve correctly located ori and ter, we calculated the distances from ori to ter in both directions on the circular genome and calcula...
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PMID: 18239897
PDF is available here.
PDF is available here.
Abstract
Our results show for the first time the effects of the phaC1-phaZ intergenic region on the substrate-dependent temporal expression of phaC1 and phaC2 genes, the repeat-unit composition of mcl-PHA, and the morphology of the PHA granules....
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PMID: 17987331
PDF is available here.
PDF is available here.
Abstract
The histone-like nucleoid-associated protein H-NS is a global transcriptional repressor that controls approximately 5% of all genes in Escherichia coli and other enterobacteria. H-NS binds to DNA with low specificity. Nonetheless, repression of some loci is exceptionally specific. Experimental data...
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PMID: 17981304
PDF is available here.
PDF is available here.
Molecular Microbiology (67)1 2008
Abstract
We report experimental analysis of transcriptional terminators in the human pathogen Helicobacter pylori. Previous bioinformatics approaches came to differing conclusions regarding transcriptional termination in this bacterium. We used a reporter construct, the tnpR-encoded resolvase, to assess term...
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PMID: 18078442
PDF is available here.
PDF is available here.
Journal of Molecular Biology (375)1 2008
Abstract
We use a combination of biochemical and genetic methods to map the p7 interaction site to within four beta' amino acid residues at the N terminus of X. oryzae RNAP beta'. The interaction site is located in an area that is close to the promoter spacer in the open complex and to the upstream boundary...
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PMID: 18021805
PDF is available here.
PDF is available here.
Microbiology (154)Pt 1 2008
Abstract
Several features distinguish laboratory and undomesticated strains of Bacillus subtilis. For example, unlike the laboratory strain 168, the undomesticated strain ATCC 6051 is deficient in sporulation in a rich sporulation medium, 2x SG. ATCC 6051 cannot induce transcription of the spoIIG operon, sug...
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PMID: 18174125
PDF is available here.
PDF is available here.
BMC Genomics (9)1 2008
Abstract
Hidden Markov Models were defined to search the T-box regulatory element and were applied to all completed prokaryotic genomes. The vast majority of the genes found downstream of the retrieved elements encoded functionalities related to transport and synthesis of amino acids and the charging of tRNA...
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PMID: 18625071
PDF is available here.
PDF is available here.
BMC Genomics (9)1 2008
Abstract
Thirty-two potential sRNAs in Streptomyces were predicted. Of these, expression of 20 was detected by microarrays and RT-PCR. The prediction was validated by a structure based computational approach. Two predicted sRNAs were found to be terminated by transcription termination factors different from...
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PMID: 18477385
PDF is available here.
PDF is available here.
Plant Physiology (145)4 2007
Abstract
We have built a collection of 36 reference Gateway entry clones carrying promoters, terminators, and reporter genes, as well as elements of the LhG4/LhGR two-component system. This collection obeys simple engineering rules. The genetic elements (parts) are designed in a standard format. They are int...
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PMID: 17965171
PDF is available here.
PDF is available here.
FEMS Microbiology Letters (276)1 2007
Abstract
These results suggested that the g1-NhaC antiporter from Bacillus sp. G1 plays a role in Na(+) extrusion at lower pH values and in pH homeostasis at pH 10 under Na(+)-limiting conditions....
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PMID: 17937670
PDF is available here.
PDF is available here.
Abstract
TRAP regulates expression of the Bacillus subtilis trpEDCFBA operon by a transcription attenuation mechanism in which tryptophan-activated TRAP binds to 11 (G/U)AG repeats in the nascent trp leader transcript. Bound TRAP blocks formation of an antiterminator structure and allows formation of an over...
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PMID: 17881743
PDF is available here.
PDF is available here.
Molecular Microbiology (66)1 2007
Abstract
We examined the effects on in vivo transcription termination of systematic base substitutions in the T/U-tract of the pyrBI attenuator. We found that these substitutions diminished transcription termination efficiency to varying extents, depending on the nature and position of the substitution. In g...
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PMID: 17725561
PDF is available here.
PDF is available here.
Molecular Cell (27)5 2007
Abstract
We report that looping is not idiosyncratic to long genes but occurs between the distal ends of genes with ORFs as short as 1 kb. Moreover, looping is dependent upon the general transcription factor TFIIB: the E62K (glutamic acid 62 --> lysine) form of TFIIB adversely affects looping at every gene t...
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PMID: 17803944
PDF is available here.
PDF is available here.
Abstract
We describe a novel method for the preparation of ANEP which maximizes the yields of recombinant peptide in a soluble and active form. A non-fusion expression plasmid pNJUTRX-1-ANEP-His(6) encoding recombinant ANEP with a His(6)-tag at its C-terminus was constructed and transformed into E. coli stra...
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PMID: 17383734
PDF is available here.
PDF is available here.
Abstract
Significant fractions of eukaryotic genomes give rise to RNA, much of which is unannotated and has reduced protein-coding potential. The genomic origins and the associations of human nuclear and cytosolic polyadenylated RNAs longer than 200 nucleotides (nt) and whole-cell RNAs less than 200 nt were...
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PMID: 17510325
PDF is available here.
PDF is available here.
Abstract
Messenger RNA transcription by Bunyaviridae family members is unique within the group of negative-strand RNA viruses as it requires on-going protein synthesis. The long-standing model explaining this phenomenon proposes that the translational requirement is not for a protein product, but instead is...
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PMID: 17400818
PDF is available here.
PDF is available here.
Molecular Microbiology (64)1 2007
Abstract
In this issue of Molecular Microbiology, Hendrickson and Lawrence analyse the sequence of bacterial genomes to map the historical traffic pattern of chromosome replication. Their surprising conclusion is that most forks terminate at the dif site rather than at the Tus/Ter sites where most investigat...
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PMID: 17376066
PDF is available here.
PDF is available here.
Molecular Microbiology (64)1 2007
Abstract
We examine bacterial genomes using bioinformatics techniques to identify the region(s) where DNA polymerase III-mediated replication has historically been terminated. We find that in both Escherichia coli and Bacillus subtilis, changes in mutational bias patterns indicate that replication terminatio...
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PMID: 17376071
PDF is available here.
PDF is available here.
Journal of General Virology (88)Pt 4 2007
Abstract
The currently available reverse-genetics systems for Influenza A virus are all based on transcription of genomic RNA by RNA polymerase I, but the species specificity of this polymerase is a disadvantage. A reverse-genetics vector containing a T7 RNA polymerase promoter, hepatitis delta virus ribozym...
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PMID: 17374773
PDF is available here.
PDF is available here.