scholarly journals The UP Element Is Necessary but Not Sufficient for Growth Rate-Dependent Control of the Escherichia coli guaB Promoter

2008 ◽  
Vol 190 (7) ◽  
pp. 2450-2457 ◽  
Author(s):  
Seyyed I. Husnain ◽  
Mark S. Thomas
Keyword(s):  
Escherichia Coli ◽  
Growth Rate ◽  
Transcription Start Site ◽  
De Novo ◽  
Start Site ◽  
Transcription Start ◽  
Lower Growth ◽  
Α Subunit ◽  
Rate Dependent ◽  
Up Elements

ABSTRACT The Escherichia coli guaB promoter (P guaB ) regulates the transcription of two genes, guaB and guaA, that are required for de novo synthesis of GMP, a precursor for the synthesis of guanine nucleoside triphosphates. The activity of P guaB is subject to growth rate-dependent control (GRDC). Here we show that the A+T-rich sequence located between positions −59 and −38 relative to the guaB transcription start site stimulates transcription from P guaB ∼8- to 10-fold and, in common with other UP elements, requires the C-terminal domain of the RNA polymerase α subunit for activity. Like the rrnB P1 UP element, the P guaB UP element contains two independently acting subsites located at positions −59 to −47 and −46 to −38 and can stimulate transcription when placed upstream of the lacP1 promoter. We reveal a novel role for the P guaB UP element by demonstrating that it is required for GRDC. The involvement of the UP element in GRDC also requires the participation of sequences located at least 100 bp upstream of the guaB transcription start site. These sequences are required for down-regulation of P guaB activity at lower growth rates.

scholarly journals Transcription Regulation by Tandem-Bound FNR at Escherichia coli Promoters

2003 ◽  
Vol 185 (20) ◽  
pp. 5993-6004 ◽  
Author(s):  
Anne M. L. Barnard ◽  
Jeffrey Green ◽  
Stephen J. W. Busby
Keyword(s):  
Escherichia Coli ◽  
Transcription Factor ◽  
Binding Site ◽  
Transcription Regulation ◽  
Transcription Start Site ◽  
Promoter Activity ◽  
Start Site ◽  
Transcription Start ◽  
Substitution Mutant

ABSTRACT FNR is an Escherichia coli transcription factor that regulates the transcription of many genes in response to anaerobiosis. We have constructed a series of artificial FNR-dependent promoters, based on the melR promoter, in which a consensus FNR binding site was centered at position −41.5 relative to the transcription start site. A second consensus FNR binding site was introduced at different upstream locations, and promoter activity was assayed in vivo. FNR can activate transcription from these promoters when the upstream FNR binding site is located at many different positions. However, sharp repression is observed when the upstream-bound FNR is located near positions −85 or −95. This repression is relieved by the FNR G74C substitution mutant, previously identified as being defective in transcription repression at the yfiD promoter. A parallel series of artificial FNR-dependent promoters, carrying a consensus FNR binding site at position −61.5 and a second upstream DNA site for FNR, was also constructed. Again, promoter activity was repressed by FNR when the upstream-bound FNR was located at particular positions.

scholarly journals Lysine Represses Transcription of the Escherichia coli dapB Gene by Preventing Its Activation by the ArgP Activator

2008 ◽  
Vol 190 (15) ◽  
pp. 5224-5229 ◽  
Author(s):  
Jean Bouvier ◽  
Patrick Stragier ◽  
Violette Morales ◽  
Elisabeth Rémy ◽  
Claude Gutierrez
Keyword(s):  
Escherichia Coli ◽  
Transcription Start Site ◽  
Biosynthetic Pathway ◽  
Genomic Library ◽  
Regulatory Region ◽  
Null Mutation ◽  
Start Site ◽  
Transcription Start ◽  
Gene Encoding ◽  
Gel Retardation Assay

ABSTRACT The Escherichia coli dapB gene encodes one of the enzymes of the biosynthetic pathway leading to lysine and its immediate precursor, diaminopimelate. Expression of dapB is repressed by lysine, but no trans-acting regulator has been identified so far. Our analysis of the dapB regulatory region shows that sequences located in the −81/−118 interval upstream of the transcription start site are essential for full expression of dapB, as well as for lysine repression. Screening a genomic library for a gene that could alleviate lysine repression when present in multicopy led to the recovery of argP, a gene encoding an activating protein of the LysR-type family, known to use lysine as an effector. An argP null mutation strongly decreases dapB transcription that becomes insensitive to lysine. Purified His6-tagged ArgP protein binds with an apparent K d of 35 nM to the dapB promoter in a gel retardation assay, provided that sequences up to −103 are present. In the presence of l-lysine and l-arginine, the binding of ArgP to dapB is partly relieved. These results fit with a model in which ArgP contributes to enhanced transcription of dapB when lysine becomes limiting.

scholarly journals Genetic Features of MCR-1-Producing Colistin-Resistant Escherichia coli Isolates in South Africa

2016 ◽  
Vol 60 (7) ◽  
pp. 4394-4397 ◽  
Author(s):  
Laurent Poirel ◽  
Nicolas Kieffer ◽  
Adrian Brink ◽  
Jennifer Coetze ◽  
Aurélie Jayol ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
South Africa ◽  
Transcription Start Site ◽  
Dna Sequences ◽  
Start Site ◽  
Transcription Start ◽  
Content Type ◽  
Promoter Sequences ◽  
Genetic Features ◽  
Community Patients

ABSTRACTA series of colistin-resistantEscherichia coliclinical isolates was recovered from hospitalized and community patients in South Africa. Seven clonally unrelated isolates harbored themcr-1gene located on different plasmid backbones. Two distinct plasmids were fully sequenced, and identical 2,600-bp-long DNA sequences defining amcr-1cassette were identified. Promoter sequences responsible for the expression ofmcr-1, deduced from the precise identification of the +1 transcription start site formcr-1, were characterized.

scholarly journals Regulation of Expression of the Region 3 Promoter of the Escherichia coli K5 Capsule Gene Cluster Involves H-NS, SlyA, and a Large 5′ Untranslated Region

2008 ◽  
Vol 191 (6) ◽  
pp. 1838-1846 ◽  
Author(s):  
Peng Xue ◽  
David Corbett ◽  
Marie Goldrick ◽  
Clare Naylor ◽  
Ian S. Roberts
Keyword(s):  
Escherichia Coli ◽  
Transcription Start Site ◽  
Untranslated Region ◽  
Regulatory Element ◽  
Gene Clusters ◽  
Regulation Of Transcription ◽  
Start Site ◽  
Transcription Start ◽  
Regulation Of Expression ◽  
Group 2

ABSTRACT Escherichia coli group 2 capsule gene clusters are temperature regulated, being expressed at 37°C but not at 20°C. Expression is regulated at the level of transcription by two convergent promoters, PR1 and PR3. In this paper, we show that regulation of transcription from PR3 involves a number of novel features including H-NS, SlyA, and a large 741-bp 5′ untranslated region (UTR). H-NS represses transcription from PR3 at 20°C and binds both 5′ and 3′ of the transcription start site. The 3′ downstream regulatory element (DRE) was essential for temperature-dependent H-NS repression. At 37°C, SlyA activates transcription independent of H-NS but maximal transcription requires H-NS. The UTR is present between the transcription start site and the first gene in the operon, kpsM. We demonstrate that the UTR, as well as containing the H-NS DRE, functions to moderate the extent of transcription that reaches kpsM and allows the binding of antitermination factor RfaH.

scholarly journals RNA Processing of Nitrogenase Transcripts in the Cyanobacterium Anabaena variabilis

2010 ◽  
Vol 192 (13) ◽  
pp. 3311-3320 ◽  
Author(s):  
Justin L. Ungerer ◽  
Brenda S. Pratte ◽  
Teresa Thiel
Keyword(s):  
Transcription Start Site ◽  
Transcription Initiation ◽  
De Novo ◽  
Start Site ◽  
Transcription Start ◽  
Stem Loop ◽  
Upstream Gene ◽  
Genes Encoding ◽  
Nitrogenase Genes ◽  
Cyanobacterium Anabaena

ABSTRACT Little is known about the regulation of nitrogenase genes in cyanobacteria. Transcription of the nifH1 and vnfH genes, encoding dinitrogenase reductases for the heterocyst-specific Mo-nitrogenase and the alternative V-nitrogenase, respectively, was studied by using a lacZ reporter. Despite evidence for a transcription start site just upstream of nifH1 and vnfH, promoter fragments that included these start sites did not drive the transcription of lacZ and, for nifH1, did not drive the expression of nifHDK1. Further analysis using larger regions upstream of nifH1 indicated that a promoter within nifU1 and a promoter upstream of nifB1 both contributed to expression of nifHDK1, with the nifB1 promoter contributing to most of the expression. Similarly, while the region upstream of vnfH, containing the putative transcription start site, did not drive expression of lacZ, the region that included the promoter for the upstream gene, ava4055, did. Characterization of the previously reported nifH1 and vnfH transcriptional start sites by 5′RACE (5′ rapid amplification of cDNA ends) revealed that these 5′ ends resulted from processing of larger transcripts rather than by de novo transcription initiation. The 5′ positions of both the vnfH and nifH1 transcripts lie at the base of a stem-loop structure that may serve to stabilize the nifHDK1 and vnfH specific transcripts compared to the transcripts for other genes in the operons providing the proper stoichiometry for the Nif proteins for nitrogenase synthesis.

scholarly journals Prosaposin: promoter analysis and central-nervous-system-preferential elements for expression in vivo

2000 ◽  
Vol 352 (2) ◽  
pp. 549-556 ◽  
Author(s):  
Ying SUN ◽  
Peng JIN ◽  
David P. WITTE ◽  
Gregory A. GRABOWSKI
Keyword(s):  
Central Nervous System ◽  
Nervous System ◽  
Transgenic Mice ◽  
Transcription Start Site ◽  
Luciferase Reporter ◽  
Start Site ◽  
Transcription Start ◽  
Α Subunit ◽  
Preferential Expression

The expression of prosaposin is temporally and spatially regulated at the transcriptional and post-translational levels. In vitro, the mouse prosaposin promoter contains functional RORE [retinoic acid-receptor-related orphan receptor α subunit (RORα)-binding element], Sp1 and U (unknown) sites within 310bp directly 5′ to the transcription start site and additional elements within 2400bp 5′ to the transcription start site. To elucidate promoter regions important to tissue-preferential expression in vivo, transgenic mice were created with 5′-flanking deletions of the prosaposin gene fused to a luciferase reporter. Nearly exclusive expression was observed in cerebrum, cerebellum and eyes of adult transgenic mice containing constructs with 234–310bp of 5ƀ-flanking DNA. This central nervous system (CNS) expression was due to the presence of RORE and overlapping Sp1 sites in this region. Internal deletion of RORE and the Sp1 cluster from the longer constructs with 2400bp of 5ƀ-flanking DNA significantly diminished expression in the CNS. The appearance of substantial visceral tissue (e.g. liver, spleen, lung, kidney, thymus and heart) expression was obtained with transgenic mice bearing constructs with 742–2400bp of 5ƀ-flanking DNA. The cellular localization of luciferase reporter-gene expression from these constructs corresponded closely with that for prosaposin. These results define important CNS and visceral regulatory regions in the promoter in vivo and may be sufficient to account for the majority of prosaposin's tissue-preferential expression.

The Mauriceville plasmid of Neurospora spp. uses novel mechanisms for initiating reverse transcription in vivo

1994 ◽  
Vol 14 (5) ◽  
pp. 3094-3107
Author(s):  
J C Kennell ◽  
H Wang ◽  
A M Lambowitz
Keyword(s):  
Reverse Transcriptase ◽  
Transcription Start Site ◽  
Reverse Transcription ◽  
De Novo ◽  
Minus Strand ◽  
Start Site ◽  
Cdna Synthesis ◽  
Transcription Start

The Mauriceville plasmid and the closely related Varkud plasmid of Neurospora spp. are retroelements that propagate in mitochondria. Replication appears to occur by a novel mechanism in which a monomer-length plasmid transcript having a 3' tRNA-like structure ending in CCA is reverse transcribed to give a full-length minus-strand cDNA beginning at or near the 3' end of the RNA. Here, we show that the plasmids are transcribed in vitro by the Neurospora mitochondrial RNA polymerase, with the major in vitro transcription start site approximately 260 bp upstream of the 5' end of the plasmid transcript. The location of the transcription start site suggests that the monomer-length transcripts are generated by transcription around the plasmid combined with a site-specific RNA cleavage after the 3'-CCA sequence. The 5' ends of minus-strand cDNAs in ribonucleoprotein particles were analyzed to obtain insight into the mechanism of initiation of reverse transcription in vivo. A major class of minus-strand cDNAs begins opposite C2 of the 3'-CCA sequence, the same site used for de novo initiation of cDNA synthesis by the plasmid reverse transcriptase in vitro. A second class of minus-strand cDNAs begins with putative primer sequences that correspond to cDNA copies of the plasmid or mitochondrial transcripts. These findings are consistent with the possibility that the plasmid reverse transcriptase initiates minus-strand cDNA synthesis in vivo both by de novo initiation and by a novel template-switching mechanism in which the 3' OH of a previously synthesized cDNA is used to prime the synthesis of a new minus-strand cDNA directly at the 3' end of the plasmid transcript.

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