scholarly journals The groESL Chaperone Operon ofLactobacillus johnsonii

1999 ◽  
Vol 65 (7) ◽  
pp. 3033-3041 ◽  
Author(s):  
D. Carey Walker ◽  
Hany S. Girgis ◽  
Todd R. Klaenhammer
Keyword(s):  
Heat Shock ◽  
Transcription Initiation ◽  
Shuttle Vector ◽  
Stress Protein ◽  
Open Reading Frames ◽  
Northern Analysis ◽  
Temperature Sensitive ◽  
Insertion Element ◽  
Translation Start ◽  
Reading Frames

ABSTRACT The Lactobacillus johnsonii VPI 11088groESL operon was localized on the chromosome near the insertion element IS1223. The operon was initially cloned as a series of three overlapping PCR fragments, which were sequenced and used to design primers to amplify the entire operon. The amplified fragment was used as a probe to recover the chromosomal copy of thegroESL operon from a partial library of L. johnsonii VPI 11088 (NCK88) DNA, cloned in the shuttle vector pTRKH2. The 2,253-bp groESL fragment contained three putative open reading frames, two of which encoded the ubiquitous GroES and GroEL chaperone proteins. Analysis of the groESLpromoter region revealed three transcription initiation sites, as well as three sets of inverted repeats (IR) positioned between the transcription and translation start sites. Two of the three IR sets bore significant homology to the CIRCE elements, implicated in negative regulation of the heat shock response in many bacteria. Northern analysis and primer extension revealed that multiple temperature-sensitive promoters preceded the groESLchaperone operon, suggesting that stress protein production in L. johnsonii is strongly regulated. Maximum groESLtranscription activity was observed following a shift to 55°C, and a 15 to 30-min exposure of log-phase cells to this temperature increased the recovery of freeze-thawed L. johnsonii VPI 11088. These results suggest that a brief, preconditioning heat shock can be used to trigger increased chaperone production and provide significant cross-protection from the stresses imposed during the production of frozen culture concentrates.

scholarly journals Dynamic Metabolic Adjustments and Genome Plasticity Are Implicated in the Heat Shock Response of the Extremely Thermoacidophilic Archaeon Sulfolobus solfataricus

2006 ◽  
Vol 188 (12) ◽  
pp. 4553-4559 ◽  
Author(s):  
Sabrina Tachdjian ◽  
Robert M. Kelly
Keyword(s):  
Stress Response ◽  
Heat Shock ◽  
Metabolic Regulation ◽  
Sulfolobus Solfataricus ◽  
Temperature Shift ◽  
Open Reading Frames ◽  
Genome Plasticity ◽  
Shock Response ◽  
Insertion Elements ◽  
Reading Frames

ABSTRACT Approximately one-third of the open reading frames encoded in the Sulfolobus solfataricus genome were differentially expressed within 5 min following an 80 to 90°C temperature shift at pH 4.0. This included many toxin-antitoxin loci and insertion elements, implicating a connection between genome plasticity and metabolic regulation in the early stages of stress response.

scholarly journals Identification of a nisI Promoter within the nisABCTIP Operon That May Enable Establishment of Nisin Immunity Prior to Induction of the Operon via Signal Transduction

2006 ◽  
Vol 188 (24) ◽  
pp. 8496-8503 ◽  
Author(s):  
Haiping Li ◽  
Daniel J. O'Sullivan
Keyword(s):  
Transcription Initiation ◽  
Start Codon ◽  
Northern Analysis ◽  
Pcr Analysis ◽  
Translation Start ◽  
Promoter Probe ◽  
Genes Encoding ◽  
Promoter Probe Vector ◽  
Successful Establishment ◽  
High Degree

ABSTRACT Certain strains of Lactococcus lactis produce the broad-spectrum bacteriocin nisin, which belongs to the lantibiotic class of antimicrobial peptides. The genes encoding nisin are organized in three contiguous operons: nisABTCIP, encoding production and immunity (nisI); nisRK, encoding regulation; and nisFEG, also involved in immunity. Transcription of nisABTCIP and nisFEG requires autoinduction by external nisin via signal transducing by NisRK. This organization poses the intriguing question of how sufficient immunity (NisI) can be expressed when the nisin cluster enters a new cell, before it encounters external nisin. In this study, Northern analysis in both Lactococcus and Enterococcus backgrounds revealed that nisI mRNA was present under conditions when no nisA transcription was occurring, suggesting an internal promoter within the operon. The nisA transcript was significantly more stable than nisI, further substantiating this. Reverse transcriptase PCR analysis revealed that the transcription initiated just upstream from nisI. Fusing this region to a lacZ gene in a promoter probe vector demonstrated that a promoter was present. The transcription start site (TSS) of the nisI promoter was mapped at bp 123 upstream of the nisI translation start codon. Ordered 5′ deletions revealed that transcription activation depended on sequences located up to bp −234 from the TSS. The presence of poly(A) tracts and computerized predictions for this region suggested that a high degree of curvature may be required for transcription initiation. The existence of this nisI promoter is likely an evolutionary adaptation of the nisin gene cluster to enable its successful establishment in other cells following horizontal transfer.

scholarly journals Regulation of transcription by Saccharomyces cerevisiae 14-3-3 proteins

2004 ◽  
Vol 382 (3) ◽  
pp. 867-875 ◽  
Author(s):  
Astrid BRUCKMANN ◽  
H. Yde STEENSMA ◽  
M. Joost TEIXEIRA de MATTOS ◽  
G. Paul H. van HEUSDEN
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Stress Response ◽  
Open Reading Frames ◽  
Ergosterol Biosynthesis ◽  
Temperature Sensitive ◽  
Regulation Of Transcription ◽  
Mrna Levels ◽  
Transcription Analysis ◽  
A Genome ◽  
Reading Frames

14-3-3 proteins form a family of highly conserved eukaryotic proteins involved in a wide variety of cellular processes, including signalling, apoptosis, cell-cycle control and transcriptional regulation. More than 150 binding partners have been found for these proteins. The yeast Saccharomyces cerevisiae has two genes encoding 14-3-3 proteins, BMH1 and BMH2. A bmh1 bmh2 double mutant is unviable in most laboratory strains. Previously, we constructed a temperature-sensitive bmh2 mutant and showed that mutations in RTG3 and SIN4, both encoding transcriptional regulators, can suppress the temperature-sensitive phenotype of this mutant, suggesting an inhibitory role of the 14-3-3 proteins in Rtg3-dependent transcription [van Heusden and Steensma (2001) Yeast 18, 1479–1491]. In the present paper, we report a genome-wide transcription analysis of a temperature-sensitive bmh2 mutant. Steady-state mRNA levels of 60 open reading frames were increased more than 2.0-fold in the bmh2 mutant, whereas those of 78 open reading frames were decreased more than 2.0-fold. In agreement with our genetic experiments, six genes known to be regulated by Rtg3 showed elevated mRNA levels in the mutant. In addition, several genes with other cellular functions, including those involved in gluconeogenesis, ergosterol biosynthesis and stress response, had altered mRNA levels in the mutant. Our data show that the yeast 14-3-3 proteins negatively regulate Rtg3-dependent transcription, stimulate the transcription of genes involved in ergosterol metabolism and in stress response and are involved in transcription regulation of multiple other genes.

Characterization, chromosomal mapping, and expression of different polyubiquitin genes in tissues from control and heat-shocked maize seedlings

1995 ◽  
Vol 73 (1-2) ◽  
pp. 19-30 ◽  
Author(s):  
Ling Liu ◽  
Daniel S. Maillet ◽  
J. Roger H. Frappier ◽  
David B. Walden ◽  
Burr G. Atkinson
Keyword(s):  
Gene Expression ◽  
Heat Shock ◽  
Open Reading Frames ◽  
Chromosomal Mapping ◽  
Animal Cells ◽  
Polyubiquitin Gene ◽  
Shock Proteins ◽  
Polyubiquitin Genes ◽  
Reading Frames ◽  
Identical Gene

Polyubiquitin transcripts accumulate in plant and animal cells following a heat shock. Most species have a few to several polyubiquitin genes; within a species, the genes may differ in nucleotide (nt) sequence and (or) the number of 228-nt repeats encoding the ubiquitin monomer. This study examines three maize (inbred Oh43) polyubiquitin genes. Two of the genes, MubG9 and MubG5, possess five repeats; the third, MubG1 possesses seven repeats. Sequence analyses of the genomic clones, MubG9 and MubG1 and a cDNA clone, MubG5, reveal that they differ primarily from each other in their nt sequences 5′ and 3′ to their open reading frames. MubG1 contains a 1004-base pair (bp) intron in its 5′ untranslated region. Using gene-specific probes, we show that the amount of polyribosome-associated mRNA transcripts from MubG9 isolated from 2- and 5-day old plumules and radicles is unchanged by heat shock. While the amount of transcript from MubG1 and MubG5 on the polyribosomes in plumules and radicles of 2-day-old seedlings is also unchanged by heat shock, the levels of these transcripts are elevated considerably in similar tissues from heat-shocked 5-day-old seedlings. Similar or identical gene-specific probes were employed to map the genes using the recombinant inbred method. MubG9 maps to chromosome 4L position 186; MubG1 maps to 5L104 and MubG5 to 4L188. The opportunity to use gene-specific probes extends the evidence for distinct modulation (time and tissue) of polyubiquitin gene expression in maize and provides the basis for locus assignment within the genome.Key words: ubiquitin, maize, heat shock, heat-shock proteins, gene expression, chromosome map.

scholarly journals Chromatin Remodeling around Nucleosome-Free Regions Leads to Repression of Noncoding RNA Transcription

2010 ◽  
Vol 30 (21) ◽  
pp. 5110-5122 ◽  
Author(s):  
Adam N. Yadon ◽  
Daniel Van de Mark ◽  
Ryan Basom ◽  
Jeffrey Delrow ◽  
Iestyn Whitehouse ◽  
...  
Keyword(s):  
Chromatin Remodeling ◽  
Transcription Initiation ◽  
Noncoding Rna ◽  
Open Reading Frames ◽  
Yeast Genome ◽  
Transcription Start Sites ◽  
Transcriptional Regulatory ◽  
First Time ◽  
Reading Frames

ABSTRACT Nucleosome-free regions (NFRs) at the 5′ and 3′ ends of genes are general sites of transcription initiation for mRNA and noncoding RNA (ncRNA). The presence of NFRs within transcriptional regulatory regions and the conserved location of transcription start sites at NFRs strongly suggest that the regulation of NFRs profoundly affects transcription initiation. To date, multiple factors are known to facilitate transcription initiation by positively regulating the formation and/or size of NFRs in vivo. However, mechanisms to repress transcription by negatively regulating the size of NFRs have not been identified. We identified four distinct classes of NFRs located at the 5′ and 3′ ends of genes, within open reading frames (ORFs), and far from ORFs. The ATP-dependent chromatin-remodeling enzyme Isw2 was found enriched at all classes of NFRs. Analysis of RNA levels also demonstrated Isw2 is required to repress ncRNA transcription from many of these NFRs. Thus, by the systematic annotation of NFRs across the yeast genome and analysis of ncRNA transcription, we established, for the first time, a mechanism by which NFR size is negatively regulated to repress ncRNA transcription from NFRs. Finally, we provide evidence suggesting that one biological consequence of repression of ncRNA, by Isw2 or by the exosome, is prevention of transcriptional interference of mRNA.

scholarly journals Characterization of pRGO1, a Plasmid from Propionibacterium acidipropionici, and Its Use for Development of a Host-Vector System in Propionibacteria

2000 ◽  
Vol 66 (11) ◽  
pp. 4688-4695 ◽  
Author(s):  
Pornpimon Kiatpapan ◽  
Yoshiteru Hashimoto ◽  
Hisako Nakamura ◽  
Yong-Zhe Piao ◽  
Hisayo Ono ◽  
...  
Keyword(s):  
Amino Acid ◽  
Shuttle Vector ◽  
Amino Acid Sequences ◽  
Open Reading Frames ◽  
Vector System ◽  
Propionibacterium Acidipropionici ◽  
Rep Protein ◽  
Gram Positive Bacteria ◽  
High Degree ◽  
Reading Frames

ABSTRACT The complete nucleotide sequence of pRGO1, a cryptic plasmid fromPropionibacterium acidipropionici E214, was determined. pRGO1 is 6,868 bp long, and its G+C content is 65.0%. Frame analysis of the sequence revealed six open reading frames, which were designated Orf1 to Orf6. The deduced amino acid sequences of Orf1 and Orf2 showed extensive similarities to an initiator of plasmid replication, the Rep protein, of various plasmids of gram-positive bacteria. The amino acid sequence of the putative translation product of orf3 exhibited a high degree of similarity to the amino acid sequences of DNA invertase in several bacteria. For the putative translation products of orf4,orf5, and orf6, on the other hand, no homologous sequences were found. The function of these open reading frames was studied by deletion analysis. A shuttle vector, pPK705, was constructed for shuttling between Escherichia coli and a Propionibacterium strain containingorf1 (repA), orf2(repB), orf5, and orf6 from pRGO1, pUC18, and the hygromycin B-resistant gene as a drug marker. Shuttle vector pPK705 successfully transformed Propionibacterium freudenreichii subsp. shermanii IFO12426 by electroporation at an efficiency of 8 × 106 CFU/μg of DNA under optimized conditions. Transformation of various species of propionibacteria with pPK705 was also performed at efficiencies of about 104 to 107 CFU/μg of DNA. The vector was stably maintained in strains of P. freudenreichiisubsp. shermanii, P. freudenreichii, P. pentosaceum, and P. freudenreichii subsp.freudenreichii grown under nonselective conditions. Successful manipulation of a host-vector system in propionibacteria should facilitate genetic studies and lead to creation of genes that are useful industrially.

scholarly journals The HlyU Protein Is a Positive Regulator of rtxA1, a Gene Responsible for Cytotoxicity and Virulence in the Human Pathogen Vibrio vulnificus

2007 ◽  
Vol 75 (7) ◽  
pp. 3282-3289 ◽  
Author(s):  
Moqing Liu ◽  
Alejandro F. Alice ◽  
Hiroaki Naka ◽  
Jorge H. Crosa
Keyword(s):  
Transcription Initiation ◽  
Vibrio Vulnificus ◽  
Protein A ◽  
Open Reading Frames ◽  
Toxin Gene ◽  
Release Factor ◽  
Rapid Progress ◽  
Human Pathogen ◽  
Opportunistic Human Pathogen ◽  
Reading Frames

ABSTRACT Vibrio vulnificus is an opportunistic human pathogen that preferentially infects compromised iron-overloaded patients, causing a fatal primary septicemia with very rapid progress, resulting in a high mortality rate. In this study we determined that the HlyU protein, a virulence factor in V. vulnificus CMCP6, up-regulates the expression of VV20479, a homologue of the Vibrio cholerae RTX (repeats in toxin) toxin gene that we named rtxA1. This gene is part of an operon together with two other open reading frames, VV20481 and VV20480, that encode two predicted proteins, a peptide chain release factor 1 and a hemolysin acyltransferase, respectively. A mutation in rtxA1 not only contributes to the loss of cytotoxic activity but also results in a decrease in virulence, whereas a deletion of VV20481 and VV20480 causes a slight decrease in virulence but with no effect in cytotoxicity. Activation of the expression of the rtxA1 operon by HlyU occurs at the transcription initiation level by binding of the HlyU protein to a region upstream of this operon.

scholarly journals utr.annotation: a tool for annotating genomic variants that could influence post-transcriptional regulation

2021 ◽  
Author(s):  
Yating Liu ◽  
Joseph D Dougherty
Keyword(s):  
R Package ◽  
Open Reading Frames ◽  
Supplementary Information ◽  
Translation Start ◽  
Upstream Open Reading Frames ◽  
Mouse Species ◽  
Translational Regulators ◽  
Post Transcriptional Regulation ◽  
Annotated Translation ◽  
Reading Frames

Abstract Summary Whole genome sequencing of patient populations is identifying thousands of new variants in UnTranslated Regions(UTRs). While the consequences of UTR mutations are not as easily predicted from primary sequence as coding mutations are, there are some known features of UTRs that modulate their function. utr.annotation is an R package that can be used to annotate potential deleterious variants in the UTR regions for both human and mouse species. Given a CSV or VCF format variant file, utr.annotation provides information of each variant on whether and how it alters known translational regulators including: upstream Open Reading Frames (uORFs), upstream Kozak sequences, polyA signals, Kozak sequences at the annotated translation start site, start codons, and stop codons, conservation scores in the variant position, and whether and how it changes ribosome loading based on a model derived from empirical data. Availability utr.annotation is freely available on Bitbucket (https://bitbucket.org/jdlabteam/utr.annotation/src/master/) and CRAN (https://cran.r-project.org/web/packages/utr.annotation/index.html) Supplementary information Supplementary data are available at https://wustl.box.com/s/yye99bryfin89nav45gv91l5k35fxo7z.

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