scholarly journals Definition of a Second Bacillus subtilis pur Regulon Comprising the pur and xpt-pbuX Operons plus pbuG, nupG (yxjA), and pbuE (ydhL)

2003 ◽  
Vol 185 (17) ◽  
pp. 5200-5209 ◽  
Author(s):  
Lars Engholm Johansen ◽  
Per Nygaard ◽  
Catharina Lassen ◽  
Yvonne Agersø ◽  
Hans H. Saxild
Keyword(s):  
Bacillus Subtilis ◽  
Amino Acid ◽  
Transcription Initiation ◽  
Indirect Evidence ◽  
Amino Acid Sequences ◽  
Common Mechanism ◽  
Nucleoside Transporter ◽  
Independent Manner ◽  
Stem Loop ◽  
Transcription Terminator

ABSTRACT In Bacillus subtilis expression of genes or operons encoding enzymes and other proteins involved in purine synthesis is affected by purine bases and nucleosides in the growth medium. The genes belonging to the PurR regulon (purR, purA, glyA, guaC, pbuO, pbuG, and the pur, yqhZ-folD, and xpt-pbuX operons) are controlled by the PurR repressor, which inhibits transcription initiation. Other genes are regulated by a less-well-described transcription termination mechanism that responds to the presence of hypoxanthine and guanine. The pur operon and the xpt-pbuX operon, which were studied here, are regulated by both mechanisms. We isolated two mutants resistant to 2-fluoroadenine in which the pur operon and the xpt-pbuX operon are expressed at increased levels in a PurR-independent manner. The mutations were caused by deletions that disrupted a potential transcription terminator structure located immediately upstream of the ydhL gene. The 5′ part of the ydhL leader region contained a 63-nucleotide (nt) sequence very similar to the 5′ ends of the leaders of the pur and xpt-pbuX operons. Transcripts of these regions may form a common tandem stem-loop secondary structure. Two additional genes with potential leader regions containing the 63-nt sequence are pbuG, encoding a hypoxanthine-guanine transporter, and yxjA, which was shown to encode a purine nucleoside transporter and is renamed nupG. Transcriptional lacZ fusions and mutations in the 63-nt sequence encoding the possible secondary structures provided evidence that expression of the pur and xpt-pbuX operons and expression of the ydhL, nupG, and pbuG genes are regulated by a common mechanism. The new pur regulon is designated the XptR regulon. Except for ydhL, the operons and genes were negatively regulated by hypoxanthine and guanine. ydhL was positively regulated. The derived amino acid sequence encoded by ydhL (now called pbuE) is similar to the amino acid sequences of metabolite efflux pumps. When overexpressed, PbuE lowers the sensitivity to purine analogs. Indirect evidence indicated that PbuE decreases the size of the internal pool of hypoxanthine. This explains why the hypoxanthine- and guanine-regulated genes are expressed at elevated levels in a mutant that overexpresses pbuE.

scholarly journals Molecular Analysis of pDL10 from Acidianus ambivalens Reveals a Family of Related Plasmids from Extremely Thermophilic and Acidophilic Archaea

Genetics ◽  
1999 ◽  
Vol 152 (4) ◽  
pp. 1307-1314
Author(s):  
Arnulf Kletzin ◽  
Angelika Lieke ◽  
Tim Urich ◽  
Robert L Charlebois ◽  
Christoph W Sensen
Keyword(s):  
Amino Acid ◽  
Regulatory Protein ◽  
Amino Acid Sequences ◽  
Open Reading Frames ◽  
Mung Bean Nuclease ◽  
Stem Loop ◽  
Rolling Circle ◽  
Rep Protein ◽  
Homologous Protein ◽  
Rep Proteins

Abstract The 7598-bp plasmid pDL10 from the extremely thermophilic, acidophilic, and chemolithoautotrophic Archaeon Acidianus ambivalens was sequenced. It contains 10 open reading frames (ORFs) organized in five putative operons. The deduced amino acid sequence of the largest ORF (909 aa) showed similarity to bacterial Rep proteins known from phages and plasmids with rolling-circle (RC) replication. From the comparison of the amino acid sequences, a novel family of RC Rep proteins was defined. The pDL10 Rep protein shared 45-80% identical residues with homologous protein genes encoded by the Sulfolobus islandicus plasmids pRN1 and pRN2. Two DNA regions capable of forming extended stem-loop structures were also conserved in the three plasmids (48-69% sequence identity). In addition, a putative plasmid regulatory protein gene (plrA) was found, which was conserved among the three plasmids and the conjugative Sulfolobus plasmid pNOB8. A homolog of this gene was also found in the chromosome of S. solfataricus. Single-stranded DNA of both pDL10 strands was detected with a mung bean nuclease protection assay using PCR detection of protected fragments, giving additional evidence for an RC mechanism of replication.

Activation domains of gene-specific transcription factors: are histones among their targets?

2004 ◽  
Vol 82 (4) ◽  
pp. 453-459 ◽  
Author(s):  
Alexandre M Erkine
Keyword(s):  
Transcription Factors ◽  
Amino Acid ◽  
Chromatin Remodeling ◽  
Transcription Initiation ◽  
Protein Complexes ◽  
Amino Acid Sequences ◽  
Gene Promoters ◽  
Activation Domain ◽  
Activation Domains ◽  
Multiple Protein

Activation domains of promoter-specific transcription factors are critical entities involved in recruitment of multiple protein complexes to gene promoters. The activation domains often retain functionality when transferred between very diverse eukaryotic phyla, yet the amino acid sequences of activation domains do not bear any specific consensus or secondary structure. Activation domains function in the context of chromatin structure and are critical for chromatin remodeling, which is associated with transcription initiation. The mechanisms of direct and indirect recruitment of chromatin-remodeling and histone-modifying complexes, including mechanisms involving direct interactions between activation domains and histones, are discussed.Key words: activation domain, transcription, chromatin, nucleosome.

scholarly journals The Membrane-Bound H+-ATPase Complex Is Essential for Growth of Lactococcus lactis

2000 ◽  
Vol 182 (17) ◽  
pp. 4738-4743 ◽  
Author(s):  
Brian J. Koebmann ◽  
Dan Nilsson ◽  
Oscar P. Kuipers ◽  
Peter R. Jensen
Keyword(s):  
Amino Acid ◽  
Lactococcus Lactis ◽  
Transcription Initiation ◽  
Northern Blot Analysis ◽  
Promoter Sequence ◽  
Initiation Site ◽  
Amino Acid Sequences ◽  
Significant Homology ◽  
Atpase Subunits ◽  
Membrane Bound

ABSTRACT The eight genes which encode the (F1Fo) H+-ATPase in Lactococcus lactis subsp.cremoris MG1363 were cloned and sequenced. The genes were organized in an operon with the gene order atpEBFHAGDC; i.e., the order of atpE and atpB is reversed with respect to the more typical bacterial organization. The deduced amino acid sequences of the corresponding H+-ATPase subunits showed significant homology with the subunits from other organisms. Results of Northern blot analysis showed a transcript at approximately 7 kb, which corresponds to the size of theatp operon. The transcription initiation site was mapped by primer extension and coincided with a standard promoter sequence. In order to analyze the importance of the H+-ATPase forL. lactis physiology, a mutant strain was constructed in which the original atp promoter on the chromosome was replaced with an inducible nisin promoter. When grown on GM17 plates the resulting strain was completely dependent on the presence of nisin for growth. These data demonstrate that the H+-ATPase is essential for growth of L. lactis under these conditions.

scholarly journals HBV Pre-S1-Derived Myristoylated Peptide (Myr47): Identification of the Inhibitory Activity on the Cellular Uptake of Lipid Nanoparticles

Viruses ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 929
Author(s):  
Masaya Nanahara ◽  
Ya-Ting Chang ◽  
Masaharu Somiya ◽  
Shun’ichi Kuroda
Keyword(s):  
Amino Acid ◽  
Cellular Uptake ◽  
Inhibitory Activity ◽  
Sodium Taurocholate ◽  
Lipid Nanoparticles ◽  
Inhibitory Effect ◽  
Amino Acid Sequences ◽  
Hbv Infection ◽  
Dependent Manner ◽  
Independent Manner

The Myr47 lipopeptide, consisting of hepatitis B virus (HBV) pre-S1 domain (myristoylated 2–48 peptide), is an effective commercialized anti-HBV drug that prevents the interaction of HBV with sodium taurocholate cotransporting polypeptide (NTCP) on human hepatocytes, an activity which requires both N-myristoylation residue and specific amino acid sequences. We recently reported that Myr47 reduces the cellular uptake of HBV surface antigen (HBsAg, subviral particle of HBV) in the absence of NTCP expression. In this study, we analyzed how Myr47 reduces the cellular uptake of lipid nanoparticles (including liposomes (LPs) and HBsAg) without NTCP expression. By using Myr47 mutants lacking the HBV infection inhibitory activity, they could reduce the cellular uptake of LPs in an N-myristoylation-dependent manner and an amino acid sequence-independent manner, not only in human liver-derived cells but also in human non-liver-derived cells. Moreover, Myr47 and its mutants could reduce the interaction of LPs with apolipoprotein E3 (ApoE3) in an N-myristoylation-dependent manner regardless of their amino acid sequences. From these results, lipopeptides are generally anchored by inserting their myristoyl residue into the lipid bilayer and can inhibit the interaction of LPs/HBsAg with apolipoprotein, thereby reducing the cellular uptake of LPs/HBsAg. Similarly, Myr47 would interact with HBV, inhibiting the uptake of HBV into human hepatic cells, while the inhibitory effect of Myr47 may be secondary to its ability to protect against HBV infection.

scholarly journals The TATA-Binding Protein (TBP) from the Human Fungal PathogenCandida albicans Can Complement Defects in Human and Yeast TBPs

1998 ◽  
Vol 180 (7) ◽  
pp. 1771-1776 ◽  
Author(s):  
Ping Leng ◽  
Philip E. Carter ◽  
Alistair J. P. Brown
Keyword(s):  
Amino Acid ◽  
Dna Binding ◽  
Transcription Initiation ◽  
Binding Protein ◽  
Tata Binding Protein ◽  
Binding Domain ◽  
Amino Acid Sequences ◽  
Initiation Factor ◽  
Dna Binding Domain

ABSTRACT Candida albicans is the major fungal pathogen in humans, yet little is known about transcriptional regulation in this organism. Therefore, we have isolated, characterized, and expressed theC. albicans TATA-binding protein (TBP) gene (TBP1), because this general transcription initiation factor plays a key role in the activation and regulation of eukaryotic promoters. Southern and Northern blot analyses suggest that a single C. albicans TBP1 locus is expressed at similar levels in the yeast and hyphal forms of this fungus. The TBP1 open reading frame is 716 bp long and encodes a functional TBP of 27 kDa. C. albicans TBP is capable of binding specifically to a TATA box in vitro, substituting for the human TBP to activate basal transcription in vitro, and suppressing the lethal Δspt15 mutation inSaccharomyces cerevisiae. The predicted amino acid sequences of TBPs from C. albicans and other organisms reveal a striking pattern of C-terminal conservation and N-terminal variability: the C-terminal DNA-binding domain displays at least 80% amino acid sequence identity to TBPs from fungi, flies, nematodes, slime molds, plants, and humans. Sequence differences between human and fungal TPBs in the DNA-binding domain may represent potential targets for antifungal therapy.

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