scholarly journals Genome-Wide Transcriptional Start Site Mapping and sRNA Identification in the Pathogen Leptospira interrogans

2017 ◽  
Vol 7 ◽  
Author(s):  
Anna Zhukova ◽  
Luis Guilherme Fernandes ◽  
Perrine Hugon ◽  
Christopher J. Pappas ◽  
Odile Sismeiro ◽  
...  
Keyword(s):  
Transcriptional Start Site ◽  
Leptospira Interrogans ◽  
Start Site ◽  
Site Mapping ◽  
Genome Wide

scholarly journals Global transcriptional start site mapping inGeobacter sulfurreducensduring growth with two different electron acceptors

2016 ◽  
Vol 363 (17) ◽  
pp. fnw175
Author(s):  
Getzabeth González ◽  
Aurora Labastida ◽  
Verónica Jímenez-Jacinto ◽  
Leticia Vega-Alvarado ◽  
Maricela Olvera ◽  
...  
Keyword(s):  
Transcriptional Start Site ◽  
Electron Acceptors ◽  
Start Site ◽  
Site Mapping

scholarly journals Identification of σE-Dependent Promoter Upstream of clpB from the Pathogenic Spirochaete Leptospira interrogans by Applying an E. coli Two-Plasmid System

2019 ◽  
Vol 20 (24) ◽  
pp. 6325
Author(s):  
Sabina Kędzierska-Mieszkowska ◽  
Katarzyna Potrykus ◽  
Zbigniew Arent ◽  
Joanna Krajewska
Keyword(s):  
Gene Expression ◽  
Gene Expression Regulation ◽  
Transcriptional Start Site ◽  
Leptospira Interrogans ◽  
Start Site ◽  
Limited Information ◽  
E Coli ◽  
Oxidative Stresses ◽  
Genetic Mechanisms ◽  
Site Identification

There is limited information on gene expression in the pathogenic spirochaete Leptospira interrogans and genetic mechanisms controlling its virulence. Transcription is the first step in gene expression that is often determined by environmental effects, including infection-induced stresses. Alterations in the environment result in significant changes in the transcription of many genes, allowing effective adaptation of Leptospira to mammalian hosts. Thus, promoter and transcriptional start site identification are crucial for determining gene expression regulation and for the understanding of genetic regulatory mechanisms existing in Leptospira. Here, we characterized the promoter region of the L. interrogans clpB gene (clpBLi) encoding an AAA+ molecular chaperone ClpB essential for the survival of this spirochaete under thermal and oxidative stresses, and also during infection of the host. Primer extension analysis demonstrated that transcription of clpB in L. interrogans initiates at a cytidine located 41 bp upstream of the ATG initiation codon, and, to a lesser extent, at an adenine located 2 bp downstream of the identified site. Transcription of both transcripts was heat-inducible. Determination of clpBLi transcription start site, combined with promoter transcriptional activity assays using a modified two-plasmid system in E. coli, revealed that clpBLi transcription is controlled by the ECF σE factor. Of the ten L. interrogans ECF σ factors, the factor encoded by LIC_12757 (LA0876) is most likely to be the key regulator of clpB gene expression in Leptospira cells, especially under thermal stress. Furthermore, clpB expression may be mediated by ppGpp in Leptospira.

scholarly journals Nascent RNA sequencing identifies a widespread sigma70-dependent pausing regulated by Gre factors in bacteria

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Zhe Sun ◽  
Alexander V. Yakhnin ◽  
Peter C. FitzGerald ◽  
Carl E. Mclntosh ◽  
Mikhail Kashlev
Keyword(s):  
Environmental Cues ◽  
Start Site ◽  
Transcription Start ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
Eukaryotic Gene Expression ◽  
Eukaryotic Gene ◽  
Vitro Analysis ◽  
In Vitro Analysis

AbstractPromoter-proximal pausing regulates eukaryotic gene expression and serves as checkpoints to assemble elongation/splicing machinery. Little is known how broadly this type of pausing regulates transcription in bacteria. We apply nascent elongating transcript sequencing combined with RNase I footprinting for genome-wide analysis of σ70-dependent transcription pauses in Escherichia coli. Retention of σ70 induces strong backtracked pauses at a 10−20-bp distance from many promoters. The pauses in the 10−15-bp register of the promoter are dictated by the canonical −10 element, 6−7 nt spacer and “YR+1Y” motif centered at the transcription start site. The promoters for the pauses in the 16−20-bp register contain an additional −10-like sequence recognized by σ70. Our in vitro analysis reveals that DNA scrunching is involved in these pauses relieved by Gre cleavage factors. The genes coding for transcription factors are enriched in these pauses, suggesting that σ70 and Gre proteins regulate transcription in response to changing environmental cues.

The two isozymes of rat intestinal alkaline phosphatase are products of two distinct genes

2000 ◽  
Vol 3 (1) ◽  
pp. 1-8 ◽  
Author(s):  
Q. XIE ◽  
D. H. ALPERS
Keyword(s):  
Alkaline Phosphatase ◽  
Transcriptional Start Site ◽  
In Vivo Studies ◽  
Peroxisome Proliferator ◽  
Start Site ◽  
Intestinal Alkaline Phosphatase ◽  
Promoter Regions ◽  
Flanking Regions

Xie, Q., and D. H. Alpers. The two isozymes of rat intestinal alkaline phosphatase are products of two distinct genes. Physiol Genomics 3: 1–8, 2000.—Rat intestinal alkaline phosphatases (IAP-I and -II) differ in primary structure, substrate specificity, tissue localization, and response to fat feeding. This study identifies two distinct genes (∼5–6 kb) corresponding to each isozyme and containing 11 exons of nearly identical size. The exon-intron junctions are identical with those found in IAP genes from other species. The 1.7 and 1.2 bp of 5′ flanking regions isolated from each gene, respectively, contain Sp1 and gut-enriched Kruppel-like factor (GKLF) binding sites, but otherwise show little identity. There is a potential CAAT-box 14 bp 5′ to the transcriptional start site, 36 bp upstream from IAP-I, and a TATA-box 31 bp 5′ to the transcriptional start site, 55 bp upstream from IAP-II. Transfection of these promoter regions (linked to luciferase as a reporter gene) into a kidney cell line, COS-7, produced the differential response to oleic acid expected from in vivo studies, i.e., threefold increase using the 5′ flanking region of IAP-II, but not IAP-I. This response was not reproduced by 5,8,11,14-eicosatetraynoic acid (ETYA) or clofibrate, suggesting that peroxisome proliferator response elements are not involved. Isolation of the IAP-II gene will allow determination of the sequences responsible for dietary fat response in the enterocyte.

scholarly journals Characterization of PmfR, the Transcriptional Activator of the pAO1-Borne purU-mabO-folD Operon of Arthrobacter nicotinovorans

2005 ◽  
Vol 187 (9) ◽  
pp. 3062-3070 ◽  
Author(s):  
Calin B. Chiribau ◽  
Cristinel Sandu ◽  
Gabor L. Igloi ◽  
Roderich Brandsch
Keyword(s):  
Binding Site ◽  
Transcriptional Start Site ◽  
Transcriptional Activator ◽  
Open Reading Frames ◽  
Start Site ◽  
Gene Encoding ◽  
Chloramphenicol Resistance ◽  
Nuclease Digestion ◽  
Arthrobacter Nicotinovorans

ABSTRACT Nicotine catabolism by Arthrobacter nicotinovorans is linked to the presence of the megaplasmid pAO1. Genes involved in this catabolic pathway are arranged on the plasmid into gene modules according to function. During nicotine degradation γ-N-methylaminobutyrate is formed from the pyrrolidine ring of nicotine. Analysis of the pAO1 open reading frames (ORF) resulted in identification of the gene encoding a demethylating γ-N-methylaminobutyrate oxidase (mabO). This gene was shown to form an operon with purU- and folD-like genes. Only in bacteria grown in the presence of nicotine could transcripts of the purU-mabO-folD operon be detected, demonstrating that this operon constitutes part of the pAO1 nicotine regulon. Its transcriptional start site was determined by primer extension analysis. Transcription of the operon was shown to be controlled by a new transcriptional regulator, PmfR, the product of a gene that is transcribed divergently from the purU, mabO, and folD genes. PmfR was purified, and electromobility shift assays and DNase I-nuclease digestion experiments were used to determine that its DNA binding site is located between −48 and −88 nucleotides upstream of the transcriptional start site of the operon. Disruption of pmfR by homologous recombination with a chloramphenicol resistance cassette demonstrated that PmfR acts in vivo as a transcriptional activator. Mutagenesis of the PmfR target DNA suggested that the sequence GTTT-14 bp-AAAC is the core binding site of the regulator upstream of the −35 promoter region of the purU-mabO-folD operon.

scholarly journals The chromatin remodeler Ino80 mediates RNAPII pausing site determination

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Youngseo Cheon ◽  
Sungwook Han ◽  
Taemook Kim ◽  
Daehee Hwang ◽  
Daeyoup Lee
Keyword(s):  
Rna Polymerase Ii ◽  
Transcriptional Start Site ◽  
Regulation Of Gene Expression ◽  
Embryonic Stem ◽  
Start Site ◽  
Chromatin Remodeler ◽  
Close Relationship ◽  
Early Transcription ◽  
Different Characteristics

Abstract Background Promoter-proximal pausing of RNA polymerase II (RNAPII) is a critical step for the precise regulation of gene expression. Despite the apparent close relationship between promoter-proximal pausing and nucleosome, the role of chromatin remodeler governing this step has mainly remained elusive. Results Here, we report highly confined RNAPII enrichments downstream of the transcriptional start site in Saccharomyces cerevisiae using PRO-seq experiments. This non-uniform distribution of RNAPII exhibits both similar and different characteristics with promoter-proximal pausing in Schizosaccharomyces pombe and metazoans. Interestingly, we find that Ino80p knockdown causes a significant upstream transition of promoter-proximal RNAPII for a subset of genes, relocating RNAPII from the main pausing site to the alternative pausing site. The proper positioning of RNAPII is largely dependent on nucleosome context. We reveal that the alternative pausing site is closely associated with the + 1 nucleosome, and nucleosome architecture around the main pausing site of these genes is highly phased. In addition, Ino80p knockdown results in an increase in fuzziness and a decrease in stability of the + 1 nucleosome. Furthermore, the loss of INO80 also leads to the shift of promoter-proximal RNAPII toward the alternative pausing site in mouse embryonic stem cells. Conclusions Based on our collective results, we hypothesize that the highly conserved chromatin remodeler Ino80p is essential in establishing intact RNAPII pausing during early transcription elongation in various organisms, from budding yeast to mouse.

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