scholarly journals Transcription of the Rod-Shaped Viruses SIRV1 and SIRV2 of the Hyperthermophilic Archaeon Sulfolobus

2004 ◽  
Vol 186 (22) ◽  
pp. 7745-7753 ◽  
Author(s):  
Alexandra Kessler ◽  
Arie B. Brinkman ◽  
John van der Oost ◽  
David Prangishvili
Keyword(s):  
Transcription Factors ◽  
Coat Protein ◽  
Single Gene ◽  
Late Phase ◽  
Promoter Sequences ◽  
Sulfolobus Islandicus ◽  
Viral Promoters ◽  
Archaeal Transcription ◽  
Transcriptional Start Sites ◽  
Time Point

ABSTRACT The double-stranded DNA genomes of the crenarchaeal rudiviruses SIRV1 (32 kb) and SIRV2 (35 kb) were previously sequenced. Here we present results of the analysis of gene expression of these viruses at different time points after infection of the host cell, Sulfolobus islandicus, and of the mapping of transcriptional start sites. Transcription of both genomes starts simultaneously at multiple sites spread over the total length of the genome and from both strands. The earliest time point when viral transcripts could be detected in cells was 30 min after infection. At this time point all the viral genes, except one, were transcribed. Many genes were clustered and appeared to be transcribed as polycistronic messengers. Although the coat protein-encoding gene was initially also transcribed as a polycistronic messenger, an abundant monocistronic transcript of this gene was detected 2 to 3 h after infection, just before assembly of viral particles. The expression of a single gene, adjacent to the coat protein gene, was upregulated at the late phase of infection, suggesting that it might be involved in specific processing and activation of the coat protein messenger. Start sites of 13 transcripts from the SIRV1 genome have been mapped by primer extension, and promoter sequences have been identified. Similar to host promoters, these viral promoters all contain potential binding sites for the archaeal transcription factors TATA binding protein and transcription factor B. In addition, most of them contain a virus-specific consensus element, suggesting the involvement of alternative transcription factors.

scholarly journals Promoter G-quadruplexes and transcription factors cooperate to shape the cell type-specific transcriptome

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Sara Lago ◽  
Matteo Nadai ◽  
Filippo M. Cernilogar ◽  
Maryam Kazerani ◽  
Helena Domíniguez Moreno ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Binding Sites ◽  
Specific Gene ◽  
Open Chromatin ◽  
Rna Seq ◽  
Transcript Levels ◽  
Promoter Sequences ◽  
G Quadruplex ◽  
Cell Type Specific ◽  
Folding State

AbstractCell identity is maintained by activation of cell-specific gene programs, regulated by epigenetic marks, transcription factors and chromatin organization. DNA G-quadruplex (G4)-folded regions in cells were reported to be associated with either increased or decreased transcriptional activity. By G4-ChIP-seq/RNA-seq analysis on liposarcoma cells we confirmed that G4s in promoters are invariably associated with high transcription levels in open chromatin. Comparing G4 presence, location and transcript levels in liposarcoma cells to available data on keratinocytes, we showed that the same promoter sequences of the same genes in the two cell lines had different G4-folding state: high transcript levels consistently associated with G4-folding. Transcription factors AP-1 and SP1, whose binding sites were the most significantly represented in G4-folded sequences, coimmunoprecipitated with their G4-folded promoters. Thus, G4s and their associated transcription factors cooperate to determine cell-specific transcriptional programs, making G4s to strongly emerge as new epigenetic regulators of the transcription machinery.

scholarly journals Cell-Free Transcription at 95°: Thermostability of Transcriptional Components and DNA Topology Requirements of Pyrococcus Transcription

Genetics ◽  
1999 ◽  
Vol 152 (4) ◽  
pp. 1325-1333
Author(s):  
Carina Hethke ◽  
Agnes Bergerat ◽  
Winfried Hausner ◽  
Patrick Forterre ◽  
Michael Thomm
Keyword(s):  
Transcription Factors ◽  
Half Life ◽  
Pyrococcus Furiosus ◽  
Polymerase Activity ◽  
Supercoiled Dna ◽  
Eukaryotic Transcription ◽  
Transcription System ◽  
Archaeal Transcription ◽  
Protein Components

Abstract Cell-free transcription of archaeal promoters is mediated by two archaeal transcription factors, aTBP and TFB, which are orthologues of the eukaryotic transcription factors TBP and TFIIB. Using the cell-free transcription system described for the hyperthermophilic Archaeon Pyrococcus furiosus by Hethke et al., the temperature limits and template topology requirements of archaeal transcription were investigated. aTBP activity was not affected after incubation for 1 hr at 100°. In contrast, the half-life of RNA polymerase activity was 23 min and that of TFB activity was 3 min. The half-life of a 328-nt RNA product was 10 min at 100°. Best stability of RNA was observed at pH 6, at 400 mm K-glutamate in the absence of Mg2+ ions. Physiological concentrations of K-glutamate were found to stabilize protein components in addition, indicating that salt is an important extrinsic factor contributing to thermostability. Both RNA and proteins were stabilized by the osmolyte betaine at a concentration of 1 m. The highest activity for RNA synthesis at 95° was obtained in the presence of 1 m betaine and 400 mm K-glutamate. Positively supercoiled DNA, which was found to exist in Pyrococcus cells, can be transcribed in vitro both at 70° and 90°. However, negatively supercoiled DNA was the preferred template at all temperatures tested. Analyses of transcripts from plasmid topoisomers harboring the glutamate dehydrogenase promoter and of transcription reactions conducted in the presence of reverse gyrase indicate that positive supercoiling of DNA inhibits transcription from this promoter.

scholarly journals Identification and Characterization of Genes Required for Cell-to-Cell Fusion in Neurospora crassa

2011 ◽  
Vol 10 (8) ◽  
pp. 1100-1109 ◽  
Author(s):  
Ci Fu ◽  
Priyadarshini Iyer ◽  
Amrita Herkal ◽  
Julia Abdullah ◽  
Angela Stout ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Transcription Factors ◽  
Neurospora Crassa ◽  
Cell Fusion ◽  
Single Gene ◽  
Vesicular Trafficking ◽  
Screening Procedure ◽  
Fusion Genes ◽  
Fusion Event ◽  
Screening Experiments

ABSTRACT A screening procedure was used to identify cell fusion (hyphal anastomosis) mutants in the Neurospora crassa single gene deletion library. Mutants with alterations in 24 cell fusion genes required for cell fusion between conidial anastomosis tubes (CATs) were identified and characterized. The cell fusion genes identified included 14 genes that are likely to function in signal transduction pathways needed for cell fusion to occur ( mik-1 , mek-1 , mak-1 , nrc-1 , mek-2 , mak-2 , rac-1 , pp2A , so/ham-1 , ham-2 , ham-3 , ham-5 , ham-9 , and mob3 ). The screening experiments also identified four transcription factors that are required for cell fusion ( adv-1 , ada-3 , rco-1 , and snf5 ). Three genes encoding proteins likely to be involved in the process of vesicular trafficking were also identified as needed for cell fusion during the screening ( amph-1 , ham-10 , pkr1 ). Three of the genes identified by the screening procedure, ham-6 , ham-7 , and ham-8 , encode proteins that might function in mediating the plasma membrane fusion event. Three of the putative signal transduction proteins, three of the transcription factors, the three putative vesicular trafficking proteins, and the three proteins that might function in mediating cell fusion had not been identified previously as required for cell fusion.

scholarly journals PRD-Containing Virulence Regulators (PCVRs) in Pathogenic Bacteria

2021 ◽  
Vol 11 ◽  
Author(s):  
Joseph S. Rom ◽  
Meaghan T. Hart ◽  
Kevin S. McIver
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Streptococcus Pyogenes ◽  
Pathogenic Bacteria ◽  
Bacterial Pathogens ◽  
Regulatory Proteins ◽  
Regulatory Domain ◽  
Modal Interaction ◽  
Promoter Sequences ◽  
Histidine Phosphorylation

Bacterial pathogens rely on a complex network of regulatory proteins to adapt to hostile and nutrient-limiting host environments. The phosphoenolpyruvate phosphotransferase system (PTS) is a conserved pathway in bacteria that couples transport of sugars with phosphorylation to monitor host carbohydrate availability. A family of structurally homologous PTS-regulatory-domain-containing virulence regulators (PCVRs) has been recognized in divergent bacterial pathogens, including Streptococcus pyogenes Mga and Bacillus anthracis AtxA. These paradigm PCVRs undergo phosphorylation, potentially via the PTS, which impacts their dimerization and their activity. Recent work with predicted PCVRs from Streptococcus pneumoniae (MgaSpn) and Enterococcus faecalis (MafR) suggest they interact with DNA like nucleoid-associating proteins. Yet, Mga binds to promoter sequences as a homo-dimeric transcription factor, suggesting a bi-modal interaction with DNA. High-resolution crystal structures of 3 PCVRs have validated the domain structure, but also raised additional questions such as how ubiquitous are PCVRs, is PTS-mediated histidine phosphorylation via potential PCVRs widespread, do specific sugars signal through PCVRs, and do PCVRs interact with DNA both as transcription factors and nucleoid-associating proteins? Here, we will review known and putative PCVRs based on key domain and functional characteristics and consider their roles as both transcription factors and possibly chromatin-structuring proteins.

scholarly journals Identification of the syr-syp Box in the Promoter Regions of Genes Dedicated to Syringomycin and Syringopeptin Production by Pseudomonas syringae pv. syringae B301D

2006 ◽  
Vol 188 (1) ◽  
pp. 160-168 ◽  
Author(s):  
Nian Wang ◽  
Shi-En Lu ◽  
Qingwu Yang ◽  
Sing-Hoi Sze ◽  
Dennis C. Gross
Keyword(s):  
Pseudomonas Syringae ◽  
Promoter Region ◽  
Genomic Island ◽  
Bioinformatic Analysis ◽  
Site Directed Mutagenesis ◽  
Signal Molecules ◽  
Promoter Regions ◽  
Promoter Sequences ◽  
Conserved Sequence ◽  
Transcriptional Start Sites

ABSTRACT The phytotoxins syringopeptin and syringomycin are synthesized by nonribosomal peptide synthetases which are encoded by the syringomycin (syr) and syringopeptin (syp) genomic island of Pseudomonas syringae pv. syringae. Previous studies demonstrated that expression of the syr-syp genes was controlled by the salA-syrF regulatory pathway, which in turn was induced by plant signal molecules. In this study, the 132-kb syr-syp genomic island was found to be organized into five polycistronic operons along with eight individual genes based on reverse transcriptional PCR and bioinformatic analysis. The transcriptional start sites of the salA gene and operons III and IV were located 63, 75, and 104 bp upstream of the start codons of salA, syrP, and syrB1, respectively, using primer extension analysis. The predicted −10/−35 promoter region of operon IV was confirmed based on deletion and site-directed mutagenesis analyses of the syrB1::uidA reporter with β-glucuronidase assays. A 20-bp conserved sequence (TGtCccgN6cggGaCA, termed the syr-syp box) with dyad symmetry around the −35 region was identified via computer analysis for the syr-syp genes/operons responsible for biosynthesis and secretion of syringomycin and syringopeptin. Expression of the syrB1::uidA fusion was decreased 59% when 6 bp was deleted from the 5′ end of the syr-syp box in the promoter region of operon IV. These results demonstrate that the conserved promoter sequences of the syr-syp genes contribute to the coregulation of syringomycin and syringopeptin production.

Interaction of CBFα/AML/PEBP2α Transcription Factors with Nucleosomes Containing Promoter Sequences Requires Flexibility in the Translational Positioning of the Histone Octamer and Exposure of the CBFα Site†

Biochemistry ◽  
2000 ◽  
Vol 39 (44) ◽  
pp. 13565-13574 ◽  
Author(s):  
José Gutiérrez ◽  
José Sierra ◽  
Ricardo Medina ◽  
Marcia Puchi ◽  
María Imschenetzky ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Promoter Sequences ◽  
Histone Octamer

scholarly journals Characterization of the Bacillus subtilis Spore Morphogenetic Coat Protein CotO

2005 ◽  
Vol 187 (24) ◽  
pp. 8278-8290 ◽  
Author(s):  
D. C. McPherson ◽  
H. Kim ◽  
M. Hahn ◽  
R. Wang ◽  
P. Grabowski ◽  
...  
Keyword(s):  
Bacillus Subtilis ◽  
Coat Protein ◽  
Late Phase ◽  
Coat Proteins ◽  
Outer Coat ◽  
Bacillus Subtilis Spore ◽  
Fluorescence And Electron Microscopy ◽  
Complex Protein ◽  
Bacillus Spores ◽  
Critical Model

ABSTRACT Bacillus spores are protected by a structurally and biochemically complex protein shell composed of over 50 polypeptide species, called the coat. Coat assembly in Bacillus subtilis serves as a relatively tractable model for the study of the formation of more complex macromolecular structures and organelles. It is also a critical model for the discovery of strategies to decontaminate B. anthracis spores. In B. subtilis, a subset of coat proteins is known to have important roles in assembly. Here we show that the recently identified B. subtilis coat protein CotO (YjbX) has an especially important morphogenetic role. We used electron and atomic force microscopy to show that CotO controls assembly of the coat layers and coat surface topography as well as biochemical and cell-biological analyses to identify coat proteins whose assembly is CotO dependent. cotO spores are defective in germination and partially sensitive to lysozyme. As a whole, these phenotypes resemble those resulting from a mutation in the coat protein gene cotH. Nonetheless, the roles of CotH and CotO and the proteins whose assembly they direct are not identical. Based on fluorescence and electron microscopy, we suggest that CotO resides in the outer coat (although not on the coat surface). We propose that CotO and CotH participate in a late phase of coat assembly. We further speculate that an important role of these proteins is ensuring that polymerization of the outer coat layers occurs in such a manner that contiguous shells, and not unproductive aggregates, are formed.

scholarly journals Making the most of methylation

eLife ◽  
2013 ◽  
Vol 2 ◽  
Author(s):  
Michiel Vermeulen
Keyword(s):  
Transcription Factors ◽  
High Throughput ◽  
High Throughput Screening ◽  
Protein Microarray ◽  
Promoter Sequences ◽  
Screening Approach

A high-throughput screening approach based on a protein microarray reveals that many human transcription factors interact specifically with methylated promoter sequences.

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