scholarly journals Nature of a paramyxovirus replication promoter influences a nearby transcription signal

2005 ◽  
Vol 86 (1) ◽  
pp. 171-180 ◽  
Author(s):  
Diane Vulliémoz ◽  
Samuel Cordey ◽  
Geneviève Mottet-Osman ◽  
Laurent Roux
Keyword(s):  
Transcription Initiation ◽  
Sendai Virus ◽  
Initiation Site ◽  
Essential Elements ◽  
Replication Initiation ◽  
Start Site ◽  
Mrna Synthesis ◽  
Gene Start ◽  
Or Gene ◽  
Transcription And Replication

The genomic and antigenomic 3′ ends of the Sendai virus replication promoters are bi-partite in nature. They are symmetrically composed of leader or trailer sequences, a gene start (gs) or gene end (ge) site, respectively, and a simple hexameric repeat. Studies of how mRNA synthesis initiates from the first gene start site (gs1) have been hampered by the fact that gs1 is located between two essential elements of the replication promoter. Transcription initiation, then, is separated from the replication initiation site by only 56 nt on the genome, so that transcription and replication may sterically interfere with each other. In order to study the initiation of Sendai virus mRNAs without this possible interference, Sendai virus mini-genomes were prepared having tandem promoters in which replication takes place from the external one, whereas mRNA synthesis occurs from the internal one. Transcription now initiates at position 146 rather than position 56 relative to the genome 3′ end. Under these conditions, it was found that the frequency with which mRNA synthesis initiates depends, in an inverse fashion, on the strength of the external replication promoter. It was also found that the sequences essential for replication are not required for basic mRNA synthesis as long as there is an external replication promoter at which viral RNA polymerase can enter the nucleocapsid template. The manner in which transcription and replication initiations influence each other is discussed.

scholarly journals Competition between the Sendai Virus N mRNA Start Site and the Genome 3′-End Promoter for Viral RNA Polymerase

2003 ◽  
Vol 77 (17) ◽  
pp. 9147-9155 ◽  
Author(s):  
Philippe Le Mercier ◽  
Dominique Garcin ◽  
Eduardo Garcia ◽  
Daniel Kolakofsky
Keyword(s):  
Rna Polymerase ◽  
Sendai Virus ◽  
Viral Rna ◽  
Promoter Strength ◽  
Start Site ◽  
Negative Effects ◽  
Gene Start ◽  
Or Gene ◽  
Insight Into ◽  
Dual Functions

ABSTRACT The genomic and antigenomic 3′-end replication promoters of Sendai virus are bipartite in nature and symmetrical, composed of le or tr sequences; a gene start or gene end site, respectively; and a simple hexameric repeat. The relative strengths of these 3′-end promoters determines the ratios of genomes and antigenomes formed during infection and whether model mini-genomes can be rescued from DNA by nondefective helper viruses. Using these tests of promoter strength, we have confirmed that tr is stronger than le in this respect. We have also found that the presence of a gene start site within either 3′-end promoter strongly reduces 3′-end promoter strength. The negative effects of the gene start site on the 3′-end promoter suggest that these closely spaced RNA start sites compete with each other for a common pool of viral RNA polymerase. The manner in which this competition could occur for polymerase off the template (in trans) and polymerase on the template (in cis) adds insight into how the viral RNA polymerase switches between its dual functions as transcriptase and replicase.

scholarly journals Core Promoter-Dependent TFIIB Conformation and a Role for TFIIB Conformation in Transcription Start Site Selection

2002 ◽  
Vol 22 (19) ◽  
pp. 6697-6705 ◽  
Author(s):  
Jennifer A. Fairley ◽  
Rachel Evans ◽  
Nicola A. Hawkes ◽  
Stefan G. E. Roberts
Keyword(s):  
Transcription Start Site ◽  
Site Selection ◽  
Transcription Initiation ◽  
Core Promoter ◽  
Initiation Site ◽  
Start Site ◽  
Wild Type ◽  
Transcription Start ◽  
General Transcription Factor ◽  
Selection Of

ABSTRACT The general transcription factor TFIIB plays a central role in the selection of the transcription initiation site. The mechanisms involved are not clear, however. In this study, we analyze core promoter features that are responsible for the susceptibility to mutations in TFIIB and cause a shift in the transcription start site. We show that TFIIB can modulate both the 5′ and 3′ parameters of transcription start site selection in a manner dependent upon the sequence of the initiator. Mutations in TFIIB that cause aberrant transcription start site selection concentrate in a region that plays a pivotal role in modulating TFIIB conformation. Using epitope-specific antibody probes, we show that a TFIIB mutant that causes aberrant transcription start site selection assembles at the promoter in a conformation different from that for wild-type TFIIB. In addition, we uncover a core promoter-dependent effect on TFIIB conformation and provide evidence for novel sequence-specific TFIIB promoter contacts.

Nucleotide sequence and transcriptional analysis of the celD β-glucanase gene from Ruminococcus flavefaciens FD-1

1995 ◽  
Vol 41 (1) ◽  
pp. 27-34 ◽  
Author(s):  
Philip E. Vercoe ◽  
Donn H. Spight ◽  
Bryan A. White
Keyword(s):  
Amino Acid ◽  
Nucleotide Sequence ◽  
Transcription Initiation ◽  
Initiation Site ◽  
Transcription Initiation Site ◽  
Start Site ◽  
Ruminococcus Flavefaciens ◽  
E Coli ◽  
Translational Start Site ◽  
Translational Start

The nucleotide sequence of the celD gene, which encodes endoglucanase and xylanase activity, from Ruminococcus flavefaciens FD-1 was determined. The DNA sequence of celD contains an open reading frame of 1215 nucleotides that encodes a polypeptide of 405 amino acids with a molecular mass of 44 631 Da. The primary amino acid sequence of CelD was screened against the GenBank data base for similar polypeptide sequences and the analysis indicated that CelD has common features with endoglucanases from the family E cellulases. Both hydrophobic cluster and BESTFIT (Genetics Computer Group (University of Wisconsin) package) analyses confirmed this relationship. Pairwise alignments using BESTFIT revealed that CelD was most closely related to endE4 from Thermomonospora fusca over a 160 amino acid window. The histidine, aspartate, and glutamate residues identified as being essential for catalytic activity in family E cellulases are conserved in CelD. A Shine–Dalgamo-like sequence was present 5 base pairs (bp) upstream of the translation start site. Primer extension analysis indicated that different transcription initiation sites are used to initiate transcription of celD in Escherichia coli and R. flavefaciens. In the case of R. flavefaciens the transcription initiation site is at a T residue (nucleotide 273) 16 bp upstream from the translational start site. A region resembling a σ70-like −10 promoter sequence is present upstream from the transcription initiation site but there is no apparent −35 region. In contrast, transcription in E. coli is initiated at a C residue 258 bp upstream from the translational start site and a sequence resembling a σ70-like −10 region is present 5 bp upstream of this residue. Assuming 17 bp is the optimal distance between −10 and −35 sites for σ70 consensus sequences, the −35 region for celD transcription initiation in E. coli would be outside the boundaries of the cloned R. flavefaciens DNA.Key words: endoglucanase, xylanase, DNA sequencing, family E cellulase.

In Vitro mRNA Synthesis by Sendai Virus: Isolation and Characterization of the Transcription Initiation Complex1

1995 ◽  
Vol 118 (2) ◽  
pp. 390-396 ◽  
Author(s):  
Toshimitsu Takagi ◽  
Kenkoh Muroya ◽  
Minako Iwama ◽  
Tatsuo Shioda ◽  
Toshihiko Tsukamoto ◽  
...  
Keyword(s):  
Transcription Initiation ◽  
Virus Isolation ◽  
Sendai Virus ◽  
Mrna Synthesis ◽  
Isolation And Characterization

scholarly journals The Critical cis-Acting Element Required for IMD2 Feedback Regulation by GDP Is a TATA Box Located 202 Nucleotides Upstream of the Transcription Start Site

2003 ◽  
Vol 23 (17) ◽  
pp. 6267-6278 ◽  
Author(s):  
Mafalda Escobar-Henriques ◽  
Bertrand Daignan-Fornier ◽  
Martine A. Collart
Keyword(s):  
Transcription Start Site ◽  
Transcription Initiation ◽  
Feedback Regulation ◽  
Initiation Site ◽  
Nutrient Sensing ◽  
Tata Box ◽  
Start Site ◽  
Sensing Element ◽  
Transcription Start ◽  
Nucleotide Synthesis

ABSTRACT Guanylic nucleotides are essential cellular players, and the critical enzyme in their tightly regulated synthesis in Saccharomyces cerevisiae is encoded by the IMD2 gene. The transcription of IMD2 is subject to general repression by nutrient limitation through the cis nutrient-sensing element. It is also subject to specific feedback regulation by the end products of the guanylic nucleotide synthesis pathway. The critical cis element for this latter mechanism is the guanine response element (GRE), a TATAATA sequence which is located 202 nucleotides upstream of the transcription initiation site and which functions as the IMD2 TATA box. We show that the GRE functions in conjunction with a 52-nucleotide stretch near the transcription start site. This very unusual promoter structure ensures low, basal expression of IMD2 and the recruitment of TFIID to the GRE in response to guanylic nucleotide limitation.

scholarly journals c-mos expression in mouse oocytes is controlled by initiator-related sequences immediately downstream of the transcription initiation site

1991 ◽  
Vol 11 (10) ◽  
pp. 5190-5196
Author(s):  
S K Pal ◽  
S S Zinkel ◽  
A A Kiessling ◽  
G M Cooper
Keyword(s):  
Transcription Start Site ◽  
Transcription Initiation ◽  
Promoter Activity ◽  
Consensus Sequence ◽  
Initiation Site ◽  
Transcription Initiation Site ◽  
Transcriptional Level ◽  
Start Site ◽  
Transcription Start ◽  
Mouse Oocytes

We have employed transient expression assays to analyze the sequences that direct c-mos transcription in mouse oocytes. Plasmids containing the chloramphenicol acetyltransferase (CAT) gene fused to either a 2.4-kb or a 731-bp fragment from the 5'-flanking region of c-mos produced similar levels of CAT activity when injected into nuclei of growing oocytes. BAL 31 deletions revealed that sequences up to 20 bp upstream of the major transcription start site could be removed without any significant loss of CAT activity. Promoter activity only decreased when these deletions closely approached the transcription start site, which was mapped at 53 nucleotides upstream of the first ATG in the c-mos open reading frame. On the other hand, deletion of sequences within 20 nucleotides downstream of the transcription initiation site resulted in a 10-fold reduction in CAT expression. A similar decrease in promoter activity was observed as a result of point mutations in these 5' untranslated sequences. Thus, sequences immediately downstream of the transcription start site, including a consensus sequence (PyPyCAPyPyPyPyPy) present in the initiator elements of several genes, appear to regulate c-mos expression in mouse oocytes. Reverse transcription-polymerase chain reaction analysis of RNA from injected oocytes showed that this regulation is manifest at the transcriptional level. Expression of c-mos in mouse oocytes thus appears to be directed by a simple promoter consisting only of sequences immediately surrounding the transcription start site, including an initiator element in the untranslated leader.

scholarly journals Roles of Human Parainfluenza Virus Type 3 Bases 13 to 78 in Replication and Transcription: Identification of an Additional Replication Promoter Element and Evidence for Internal Transcription Initiation

2006 ◽  
Vol 80 (11) ◽  
pp. 5388-5396 ◽  
Author(s):  
Michael A. Hoffman ◽  
LeeAnne M. Thorson ◽  
John E. Vickman ◽  
Joseph S. Anderson ◽  
Nathan A. May ◽  
...  
Keyword(s):  
Virus Type ◽  
Transcription Initiation ◽  
Point Mutations ◽  
Parainfluenza Virus ◽  
N Gene ◽  
Intergenic Sequence ◽  
Gene Start ◽  
Human Parainfluenza Virus ◽  
Type 3 ◽  
Transcription And Replication

ABSTRACT The genomic promoter of human parainfluenza virus type 3 (HPIV3) contains multiple cis-elements controlling transcription and replication. Previous work showed that regions 1 to 12 and 79 to 96 were critical in promoting replication of an HPIV3 minireplicon, while the intergenic sequence and N gene start signal (IS/Ngs, bases 49 to 61) were important for transcription. Because these data were collected primarily using point mutations, not every base from position 1 to 96 was analyzed, and some important control elements may have been missed. To clarify the role of bases 13 to 78 in transcription and replication, a series of mutations were made which collectively scanned this entire region. Mutation of bases 13 to 28 resulted in markedly decreased HPIV3 minireplicon replication, indicating these bases constitute an additional cis-element involved in the synthesis of the HPIV3 antigenomic RNA. The position dependence of the IS/Ngs was also examined. Analysis of mutants in which the IS/Ngs was shifted 5′ or 3′ showed that this segment could be moved without significantly disrupting transcription initiation. Additional mutants which contained two successive IS/Ngs segments were created to test whether the polymerase accessed the gene start signal by proceeding along the template 3′ to 5′ or by binding internally at the gene start signal. Based on analysis of the double gene start mutants, we propose a model of internal transcription initiation in which the polymerase enters the template at approximately the location of the natural N gene start but then scans the template bidirectionally to find a gene start signal and initiate transcription.

scholarly journals Primary and Secondary Structural Elements Required for Synthesis of Barley Yellow Dwarf Virus Subgenomic RNA1

1999 ◽  
Vol 73 (4) ◽  
pp. 2876-2885 ◽  
Author(s):  
Gennadiy Koev ◽  
B. R. Mohan ◽  
W. Allen Miller
Keyword(s):  
Secondary Structure ◽  
Transcription Initiation ◽  
Initiation Site ◽  
Yellow Dwarf ◽  
Replicase Gene ◽  
Start Site ◽  
Genomic Rna ◽  
Computer Prediction ◽  
Barley Yellow Dwarf ◽  
Promoter Recognition

ABSTRACT Barley yellow dwarf luteovirus (BYDV) generates three 3′-coterminal subgenomic RNAs (sgRNAs) in infected cells. The promoter of sgRNA1 is a putative hot spot for RNA recombination in luteovirus evolution. The sgRNA1 transcription start site was mapped previously to either nucleotide 2670 or nucleotide 2769 of BYDV genomic RNA (gRNA) in two independent studies. Our data support the former initiation site. The boundaries of the sgRNA1 promoter map between nucleotides 2595 and 2692 on genomic RNA. Computer prediction, phylogenetic comparison, and structural probing revealed two stem-loops (SL1 and SL2) in the sgRNA1 promoter region on the negative strand. Promoter function was analyzed by inoculating protoplasts with a full-length infectious clone of the BYDV genome containing mutations in the sgRNA promoter. Because the promoter is located in an essential coding region of the replicase gene, we duplicated it in a nonessential part of the genome from which a new sgRNA was expressed. Mutational analysis revealed that secondary structure, but not the nucleotide sequence, was important at the base of SL1. Regions with both RNA primary and secondary structural features that contributed to transcription initiation were found at the top of SL1. Primary sequence, but not the secondary structure, was required in SL2, which includes the initiation site. Disruption of base pairing near the sgRNA1 start site increased the level of transcription three- to fourfold. We propose that both primary and secondary structures of the sgRNA1 promoter of BYDV play unique roles in sgRNA1 promoter recognition and transcription initiation.

DNA sequence and transcriptional characterization of a β-glucanase gene (celB) fromRuminococcus flavefaciensFD-1

1995 ◽  
Vol 41 (10) ◽  
pp. 869-876 ◽  
Author(s):  
Philip E. Vercoe ◽  
Jennie L. Finks ◽  
Bryan A. White
Keyword(s):  
Transcription Initiation ◽  
Initiation Site ◽  
Primer Extension ◽  
Start Site ◽  
Translation Start Site ◽  
Ruminococcus Flavefaciens ◽  
Endoglucanase Activity ◽  
Hydrophobic Cluster Analysis ◽  
E Coli ◽  
Translation Start

The recombinant clone pBAW101 (in pBluescript SK–) contains the celB endoglucanase gene from Ruminococcus flavefaciens FD-1. Subcloning indicated that the endoglucanase activity expressed was present within a 2.4-kb insert (pBAW104). The nucleotide sequence of the celB gene was determined, and upon analysis, revealed an open reading frame of 1943 nucleotides that encodes a polypeptide of 632 amino acids with a molecular weight of 69 414. A putative Shine–Dalgarno sequence was identified 6 bp upstream from the translation start site. The N-terminal 32 amino acid residues were typical of prokaryotic signal sequences. Hydrophobic cluster analysis (HCA) and DNA alignment of CelB to other published β-glucanase polypeptide sequences in GenBank indicate that CelB belongs in HCA cellulase family 44. Primer extension analyses were performed using RNA isolated from R. flavefaciens grown on cellulose and cellobiose, and from Escherichia coli containing the plasmid clone pBAW104. Transcription is initiated at different sites in E. coli and R. flavefaciens. In the case of R. flavefaciens transcription is initiated at a C residue (nucleotides 329), 221 bp upstream from the translation start site. There were no regions resembling E. coli σ70-like promoter sequences present upstream from this putative transcription initiation site. In contrast, numerous transcription initiation sites were identified when RNA from E. coli was used in the primer extension analyses.Key words: Ruminococcus flavefaciens, endoglucanase, transcription, family 44 endoglucanase.

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