scholarly journals Rho-dependent terminators and transcription termination

Microbiology ◽  
2006 ◽  
Vol 152 (9) ◽  
pp. 2515-2528 ◽  
Author(s):  
M. Sofia Ciampi
Keyword(s):  
Enteric Bacteria ◽  
Essential Elements ◽  
Site Directed Mutagenesis ◽  
Regulatory Mechanisms ◽  
Coding Sequences ◽  
Gram Positive Bacteria ◽  
Sequence Elements ◽  
Additional Sequence ◽  
Mrna Binding ◽  
Termination Process

Rho-dependent transcription terminators participate in sophisticated genetic regulatory mechanisms, in both bacteria and phages; they occur in regulatory regions preceding the coding sequences of genes and within coding sequences, as well as at the end of transcriptional units, to prevent readthrough transcription. Most Rho-dependent terminators have been found in enteric bacteria, but they also occur in Gram-positive bacteria and may be widespread among bacteria. Rho-dependent termination requires both cis-acting elements, on the mRNA, and trans-acting factors. The only cis-acting element common to Rho-dependent terminators is richness in rC residues. Additional sequence elements have been observed at different Rho termination sites. These ‘auxiliary elements' may assist in the termination process; they differ among terminators, their occurrence possibly depending on the function and sequence context of the terminator. Specific nucleotides required for termination have also been identified at Rho sites. Rho is the main factor required for termination; it is a ring-shaped hexameric protein with ATPase and helicase activities. NusG, NusA and NusB are additional factors participating in the termination process. Rho-dependent termination occurs by binding of Rho to ribosome-free mRNA, C-rich sites being good candidates for binding. Rho's ATPase is activated by Rho–mRNA binding, and provides the energy for Rho translocation along the mRNA; translocation requires sliding of the message into the central hole of the hexamer. When a polymerase pause site is encountered, the actual termination occurs, and the transcript is released by Rho's helicase activity. Many aspects of this process are still being studied. The isolation of mutants suppressing termination, site-directed mutagenesis of cis-acting elements in Rho-dependent termination, and biochemistry, are and will be contributing to unravelling the still undefined aspects of the Rho termination machinery. Analysis of the more sophisticated regulatory mechanisms relying on Rho-dependent termination may be crucial in identifying new essential elements for termination.

scholarly journals Draft Genome Sequence of Enterococcus faecalis DD14, a Bacteriocinogenic Lactic Acid Bacterium with Anti-Clostridium Activity

2017 ◽  
Vol 5 (30) ◽  
Author(s):  
Yanath Belguesmia ◽  
Valérie Leclère ◽  
Matthieu Duban ◽  
Eric Auclair ◽  
Djamel Drider
Keyword(s):  
Lactic Acid ◽  
Lactic Acid Bacterium ◽  
Enterococcus Faecalis ◽  
Genome Sequence ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Coding Sequences ◽  
Content Type ◽  
Gram Positive Bacteria ◽  
Healthy Newborn

ABSTRACT We report the draft genome sequence of Enterococcus faecalis DD14, a strain isolated from meconium of a healthy newborn at Roubaix Hospital (France). The strain displayed antagonism against a set of Gram-positive bacteria through concomitant production of lactic acid and bacteriocin. The genome has a size of 2,893,365 bp and a 37.3% G+C ratio and is predicted to contain at least 2,755 coding sequences and 62 RNAs.

scholarly journals PATACSDB - The database of polyA translational attenuators in coding sequences

2015 ◽  
Author(s):  
Malgorzata Habich ◽  
Sergej Djuranovic ◽  
Pawel Szczesny
Keyword(s):  
Gene Dosage ◽  
Interesting Case ◽  
Minimal Length ◽  
Regulatory Mechanisms ◽  
Coding Sequences ◽  
Translation Apparatus ◽  
Recent Addition ◽  
Dosage Balance ◽  
The Stability ◽  
Eukaryotic Genomes

Recent addition to the repertoire of gene expression regulatory mechanisms are polyadenylate (polyA) tracks encoding for poly-lysine runs in protein sequences. Such tracks stall translation apparatus and induce frameshifting independently of the effects of charged nascent poly-lysine sequence on the ribosome exit channel. As such they substantially influence the stability of mRNA and amount of protein produced from a given transcript. Single base changes in these regions are enough to exert a measurable response on both protein and mRNA abundance, and makes each of these sequences potentially interesting case studies for effects of synonymous mutation, gene dosage balance and natural frameshifting. Here we present the PATACSDB, a resource that contain comprehensive list of polyA tracks from over 250 eukaryotic genomes. Our data is based on Ensembl genomic database of coding sequences and filtered with algorithm of 12A-1 which selects sequences of polyA tracks with a minimal length of 12 A's allowing for one mismatched base. The PATACSDB database is accesible at: http://sysbio.ibb.waw.pl/patacsdb. Source code is available for download from GitHub repository at http://github.com/habich/PATACSDB, including the scripts to recreate the database from the scratch on user's own computer.

scholarly journals NS1′ of Flaviviruses in the Japanese Encephalitis Virus Serogroup Is a Product of Ribosomal Frameshifting and Plays a Role in Viral Neuroinvasiveness

2009 ◽  
Vol 84 (3) ◽  
pp. 1641-1647 ◽  
Author(s):  
Ezequiel Balmori Melian ◽  
Edward Hinzman ◽  
Tomoko Nagasaki ◽  
Andrew E. Firth ◽  
Norma M. Wills ◽  
...  
Keyword(s):  
Japanese Encephalitis Virus ◽  
Japanese Encephalitis ◽  
Nonstructural Protein ◽  
Infectious Clone ◽  
Encephalitis Virus ◽  
Innate Immune ◽  
Site Directed Mutagenesis ◽  
Sequence Elements ◽  
Rna Pseudoknot ◽  
Frameshift Event

ABSTRACT Flavivirus NS1 is a nonstructural protein involved in virus replication and regulation of the innate immune response. Interestingly, a larger NS1-related protein, NS1′, is often detected during infection with the members of the Japanese encephalitis virus serogroup of flaviviruses. However, how NS1′ is made and what role it performs in the viral life cycle have not been determined. Here we provide experimental evidence that NS1′ is the product of a −1 ribosomal frameshift event that occurs at a conserved slippery heptanucleotide motif located near the beginning of the NS2A gene and is stimulated by a downstream RNA pseudoknot structure. Using site-directed mutagenesis of these sequence elements in an infectious clone of the Kunjin subtype of West Nile virus, we demonstrate that NS1′ plays a role in viral neuroinvasiveness.

scholarly journals Ultraconserved Non-coding DNA Within Diptera and Hymenoptera

2020 ◽  
Vol 10 (9) ◽  
pp. 3015-3024 ◽  
Author(s):  
Thomas Brody ◽  
Amarendra Yavatkar ◽  
Alexander Kuzin ◽  
Ward F Odenwald
Keyword(s):  
Genomic Sequence ◽  
Mosquito Species ◽  
Phylogenetic Footprinting ◽  
Reference Sequence ◽  
Phylogenetic Groups ◽  
Developmental Genes ◽  
Coding Sequences ◽  
Conserved Sequence ◽  
Sequence Elements ◽  
And Function

Abstract This study has taken advantage of the availability of the assembled genomic sequence of flies, mosquitos, ants and bees to explore the presence of ultraconserved sequence elements in these phylogenetic groups. We compared non-coding sequences found within and flanking Drosophila developmental genes to homologous sequences in Ceratitis capitata and Musca domestica. Many of the conserved sequence blocks (CSBs) that constitute Drosophila cis-regulatory DNA, recognized by EvoPrinter alignment protocols, are also conserved in Ceratitis and Musca. Also conserved is the position but not necessarily the orientation of many of these ultraconserved CSBs (uCSBs) with respect to flanking genes. Using the mosquito EvoPrint algorithm, we have also identified uCSBs shared among distantly related mosquito species. Side by side comparison of bee and ant EvoPrints of selected developmental genes identify uCSBs shared between these two Hymenoptera, as well as less conserved CSBs in either one or the other taxon but not in both. Analysis of uCSBs in these dipterans and Hymenoptera will lead to a greater understanding of their evolutionary origin and function of their conserved non-coding sequences and aid in discovery of core elements of enhancers. This study applies the phylogenetic footprinting program EvoPrinter to detection of ultraconserved non-coding sequence elements in Diptera, including flies and mosquitos, and Hymenoptera, including ants and bees. EvoPrinter outputs an interspecies comparison as a single sequence in terms of the input reference sequence. Ultraconserved sequences flanking known developmental genes were detected in Ceratitis and Musca when compared with Drosophila species, in Aedes and Culex when compared with Anopheles, and between ants and bees. Our methods are useful in detecting and understanding the core evolutionarily hardened sequences required for gene regulation.

scholarly journals Sheep elastin genes. Isolation and preliminary characterization of a 9.9-kilobase genomic clone

1984 ◽  
Vol 220 (3) ◽  
pp. 643-652 ◽  
Author(s):  
J M Davidson ◽  
S Shibahara ◽  
M P Schafer ◽  
M Harrison ◽  
C Leach ◽  
...  
Keyword(s):  
Genomic Dna ◽  
Southern Blotting ◽  
Genomic Library ◽  
Base Pairs ◽  
Coding Sequences ◽  
Restriction Fragments ◽  
Sequence Elements ◽  
The Right ◽  
Elastin Gene

A sheep genomic library containing sheep DNA in the bacteriophage vector Charon 4A was screened for elastin-gene sequences with partially purified, 32P-labelled elastin mRNA (mRNAE). A recombinant containing a 9.9-kb (kilobase) insert was selected from several positive clones by secondary and tertiary screening for further characterization. Positive identification of this elastin clone, designated SE1, was made with radiolabelled mRNAE by hydridization-selected translation and Southern blotting of restriction-enzyme fragments of SE1 DNA. Hybridization of either mRNAE or elastin complementary DNA to restriction fragments of SE1 showed that most of these fragments of SE1 contained elastin-coding sequences. Orientation of the insert was established by preferential hybridization of a short complementary elastin DNA to restriction fragments adjacent to the right arm of Charon 4A. Reciprocal hybridizations of nick-translated SE1 and sheep genomic DNA on Southern blots showed that two restriction fragments of SE1 contained sequence elements which were repeated at high frequency in a restriction-endonuclease-EcoR1 digest of total sheep genomic DNA. In the accompanying paper [Davidson, Shibahara, Boyd, Mason, Tolstoshev & Crystal (1984) Biochem. J. 220, 653-663], it is shown that a subcloned fragment of this elastin gene quantitatively and specifically hybridized to mRNAE sequences in sheep tissue RNA. Electron microscopy of SE1-mRNAE hybrids indicated the presence of at least seven large R-loops. Measurements of these structures indicated that SE1 is likely to contain less than 2 kb of coding sequence and more than 8 kb of intervening sequence, with an average exon size of 120 base-pairs. Thus the elastin gene is distributed over an extended region of the sheep genome and contains numerous intervening and coding sequences.

scholarly journals A Region of Bacillus subtilis CodY Protein Required for Interaction with DNA

2005 ◽  
Vol 187 (12) ◽  
pp. 4127-4139 ◽  
Author(s):  
Pascale Joseph ◽  
Manoja Ratnayake-Lecamwasam ◽  
Abraham L. Sonenshein
Keyword(s):  
Bacillus Subtilis ◽  
Dna Binding ◽  
Dna Recognition ◽  
Transcriptional Regulators ◽  
Site Directed Mutagenesis ◽  
Regulation Of Transcription ◽  
Gram Positive Bacteria ◽  
Target Promoters

ABSTRACT Bacillus subtilis CodY protein is the best-studied member of a novel family of global transcriptional regulators found ubiquitously in low-G+C gram-positive bacteria. As for many DNA-binding proteins, CodY appears to have a helix-turn-helix (HTH) motif thought to be critical for interaction with DNA. This putative HTH motif was found to be highly conserved in the CodY homologs. Site-directed mutagenesis was used to identify amino acids within this motif that are important for DNA recognition and binding. The effects of each mutation on DNA binding in vitro and on the regulation of transcription in vivo from two target promoters were tested. Each of the mutations had similar effects on binding to the two promoters in vitro, but some mutations had differential effects in vivo.

scholarly journals A short 5'-flanking region mediates glucose repression of amylase gene expression in Drosophila melanogaster.

Genetics ◽  
1993 ◽  
Vol 134 (2) ◽  
pp. 507-515 ◽  
Author(s):  
C Magoulas ◽  
L Bally-Cuif ◽  
A Loverre-Chyurlia ◽  
B Benkel ◽  
D Hickey
Keyword(s):  
Drosophila Melanogaster ◽  
Dna Sequences ◽  
Glucose Repression ◽  
Essential Elements ◽  
Site Directed Mutagenesis ◽  
Deletion Analysis ◽  
Upstream Region ◽  
Directed Mutagenesis ◽  
Amylase Gene ◽  
Recombinant Gene

Abstract Expression of the alpha-amylase gene is highly repressed by dietary glucose in Drosophila melanogaster larvae. Here, we show that glucose repression is controlled by DNA sequences that are located upstream of the transcribed region. Recombinant gene constructions, in which the amylase promoter sequences were fused with the transcribed region of the Adh gene, were expressed in transgenic Drosophila larvae. The expression of ADH from the recombinant gene was shown to be subject to glucose repression. The function of potential regulatory cis-acting elements within the glucose responsive upstream region was examined by deletion analysis and by site-directed mutagenesis, coupled with expression assays in transformed larvae. The upstream deletion analysis showed that essential elements, both for overall activity and for glucose repression of the amylase gene, are located within a 109-bp region upstream of the transcription start site. Site-directed mutagenesis of these upstream sequences showed that the TATA motif, at position -31, and a novel 36-bp element, at position -109, were necessary for full activity of the amylase promoter. None of the introduced mutations resulted in loss of glucose responsiveness. These results indicate that glucose repression, in Drosophila, is mediated by transcriptional mechanisms that involve multiple, functionally redundant DNA elements.

Identification of a key integrin-binding sequence in VCAM-1 homologous to the LDV active site in fibronectin

1994 ◽  
Vol 107 (8) ◽  
pp. 2127-2135 ◽  
Author(s):  
J.M. Clements ◽  
P. Newham ◽  
M. Shepherd ◽  
R. Gilbert ◽  
T.J. Dudgeon ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Active Sites ◽  
Site Directed Mutagenesis ◽  
Immunoglobulin Superfamily ◽  
Adhesion Receptor ◽  
Ligand Binding Sites ◽  
Dependent Cell ◽  
Additional Sequence ◽  
Binding Sequence ◽  
Distinct Peptide

The integrin adhesion receptor alpha 4 beta 1 binds two ligands, the extracellular matrix glycoprotein fibronectin and the immunoglobulin superfamily member VCAM-1. Ligand-binding sites are contained with the HepII/IIICS domain of fibronectin, and within the homologous immunoglobulin domains 1 and 4 of VCAM-1. Previous studies have shown that the binding of each ligand to alpha 4 beta 1 is mutually exclusive, suggesting that they may employ similar mechanisms to bind receptor. Fibronectin contains at least three distinct peptide sequences that are active sites for alpha 4 beta 1 binding, two homologous sequences Leu-Asp-Val-Pro (LDVP) and Ile-Asp-Ala-Pro (IDAP), and a third related to Arg-Gly-Asp (RGD). Using a combination of site-directed mutagenesis and synthetic peptide approaches in conjunction with VCAM-1-dependent cell adhesion assays, we now report the identification of a key alpha 4 beta 1-binding sequence in both domains 1 and 4 of VCAM-1 as the tetrapeptide Ile-Asp-Ser-Pro (IDSP). Mutagenesis studies also suggest that an additional sequence in domain 1, KLEK, participates in receptor binding. Since IDSP is homologous to the LDVP and IDAP fibronectin peptides, this therefore provides a molecular explanation for the promiscuity of ligand binding by alpha 4 beta 1 and has implications for the design of synthetic VCAM-1 antagonists. The extrapolation of these findings to other integrin-binding immunoglobulin ligands is also discussed.

scholarly journals Membrane trafficking of the bacterial adhesin GspB and the accessory Sec transport machinery

2018 ◽  
Vol 294 (5) ◽  
pp. 1502-1515 ◽  
Author(s):  
Cierra Spencer ◽  
Barbara A. Bensing ◽  
Nagendra N. Mishra ◽  
Paul M. Sullam
Keyword(s):  
Signal Peptide ◽  
Membrane Trafficking ◽  
Lipid Membranes ◽  
Large Cell ◽  
Lipid Binding ◽  
Site Directed Mutagenesis ◽  
Host Cells ◽  
Hydrophobic Core ◽  
Gram Positive Bacteria ◽  
Anionic Lipids

The serine-rich repeat (SRR) glycoproteins of Gram-positive bacteria are large, cell wall–anchored adhesins that mediate binding to many host cells and proteins and are associated with bacterial virulence. SRR glycoproteins are exported to the cell surface by the accessory Sec (aSec) system comprising SecA2, SecY2, and 3–5 additional proteins (Asp1 to Asp5) that are required for substrate export. These adhesins typically have a 90-amino acid-long signal peptide containing an elongated N-region and a hydrophobic core. Previous studies of GspB (the SRR adhesin ofStreptococcus gordonii) have shown that a glycine-rich motif in its hydrophobic core is essential for selective, aSec-mediated transport. However, the role of this extended N-region in transport is poorly understood. Here, using protein–lipid co-flotation assays and site-directed mutagenesis, we report that the N-region of the GspB signal peptide interacts with anionic lipids through electrostatic forces and that this interaction is necessary for GspB preprotein trafficking to lipid membranes. Moreover, we observed that protein–lipid binding is required for engagement of GspB with SecA2 and for aSec-mediated transport. We further found that SecA2 and Asp1 to Asp3 also localize selectively to liposomes that contain anionic lipids. These findings suggest that the GspB signal peptide electrostatically binds anionic lipids at the cell membrane, where it encounters SecA2. After SecA2 engagement with the signal peptide, Asp1 to Asp3 promote SecA2 engagement with the mature domain, which activates GspB translocation.

Sign in / Sign up

Export Citation Format

Share Document