The cutting edge of archaeal transcription

The archaeal RNA polymerase (RNAP) is a double-psi β-barrel enzyme closely related to eukaryotic RNAPII in terms of subunit composition and architecture, promoter elements and basal transcription factors required for the initiation and elongation phase of transcription. Understanding archaeal transcription is, therefore, key to delineate the universally conserved fundamental mechanisms of transcription as well as the evolution of the archaeo-eukaryotic transcription machineries. The dynamic interplay between RNAP subunits, transcription factors and nucleic acids dictates the activity of RNAP and ultimately gene expression. This review focusses on recent progress in our understanding of (i) the structure, function and molecular mechanisms of known and less characterized factors including Elf1 (Elongation factor 1), NusA (N-utilization substance A), TFS4, RIP and Eta, and (ii) their evolution and phylogenetic distribution across the expanding tree of Archaea.

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

Genetics ◽

10.1093/genetics/152.4.1325 ◽

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.

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Small-Molecule Hormones: Molecular Mechanisms of Action

International Journal of Endocrinology ◽

10.1155/2013/601246 ◽

2013 ◽

Vol 2013 ◽

pp. 1-21 ◽

Cited By ~ 10

Author(s):

Monika Puzianowska-Kuznicka ◽

Eliza Pawlik-Pachucka ◽

Magdalena Owczarz ◽

Monika Budzińska ◽

Jacek Polosak

Keyword(s):

Transcription Factors ◽

Small Molecule ◽

Molecular Mechanisms ◽

Hormone Receptors ◽

Target Genes ◽

Direct Interaction ◽

Nuclear Hormone Receptors ◽

Membrane Phospholipids ◽

Basal Transcription Factors ◽

Hormonal Stimulus

Small-molecule hormones play crucial roles in the development and in the maintenance of an adult mammalian organism. On the molecular level, they regulate a plethora of biological pathways. Part of their actions depends on their transcription-regulating properties, exerted by highly specific nuclear receptors which are hormone-dependent transcription factors. Nuclear hormone receptors interact with coactivators, corepressors, basal transcription factors, and other transcription factors in order to modulate the activity of target genes in a manner that is dependent on tissue, age and developmental and pathophysiological states. The biological effect of this mechanism becomes apparent not earlier than 30–60 minutes after hormonal stimulus. In addition, small-molecule hormones modify the function of the cell by a number of nongenomic mechanisms, involving interaction with proteins localized in the plasma membrane, in the cytoplasm, as well as with proteins localized in other cellular membranes and in nonnuclear cellular compartments. The identity of such proteins is still under investigation; however, it seems that extranuclear fractions of nuclear hormone receptors commonly serve this function. A direct interaction of small-molecule hormones with membrane phospholipids and with mRNA is also postulated. In these mechanisms, the reaction to hormonal stimulus appears within seconds or minutes.

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Translation Elongation Factor 4 (LepA) Contributes to Tetracycline Susceptibility by Stalling Elongating Ribosomes

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.02356-17 ◽

2018 ◽

Vol 62 (8) ◽

Cited By ~ 3

Author(s):

Bin Liu ◽

Chunlai Chen

Keyword(s):

Protein Synthesis ◽

Ribosome Biogenesis ◽

Molecular Mechanisms ◽

Elongation Factor ◽

Ribosome Profiling ◽

Translation Elongation Factor ◽

Translation Elongation ◽

Content Type ◽

Elongation Phase ◽

Profiling Analysis

ABSTRACTEven though elongation factor 4 (EF4) is the third most conserved protein in bacteria, its physiological functions remain largely unknown and its proposed molecular mechanisms are conflicting among previous studies. In the present study, we show that the growth of anEscherichia colistrain is more susceptible to tetracycline than its EF4 knockout strain. Consistent with previous studies, our results suggested that EF4 affects ribosome biogenesis when tetracycline is present. Through ribosome profiling analysis, we discovered that EF4 causes 1-nucleotide shifting of ribosomal footprints on mRNA when cells have been exposed to tetracycline. In addition, when tetracycline is present, EF4 inhibits the elongation of protein synthesis, which leads to the accumulation of ribosomes in the early segment of mRNA. Altogether, when cells are exposed to tetracycline, EF4 alters both ribosome biogenesis and the elongation phase of protein synthesis.

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TFE and Spt4/5 open and close the RNA polymerase clamp during the transcription cycle

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1515817113 ◽

2016 ◽

Vol 113 (13) ◽

pp. E1816-E1825 ◽

Cited By ~ 43

Author(s):

Sarah Schulz ◽

Andreas Gietl ◽

Katherine Smollett ◽

Philip Tinnefeld ◽

Finn Werner ◽

...

Keyword(s):

Transcription Factors ◽

Nucleic Acids ◽

Single Molecule ◽

Conformational Changes ◽

Molecular Mechanisms ◽

Conformational Space ◽

Single Molecule Fret ◽

Transcription Complexes ◽

Basal Transcription Factors ◽

Transcription Cycle

Transcription is an intrinsically dynamic process and requires the coordinated interplay of RNA polymerases (RNAPs) with nucleic acids and transcription factors. Classical structural biology techniques have revealed detailed snapshots of a subset of conformational states of the RNAP as they exist in crystals. A detailed view of the conformational space sampled by the RNAP and the molecular mechanisms of the basal transcription factors E (TFE) and Spt4/5 through conformational constraints has remained elusive. We monitored the conformational changes of the flexible clamp of the RNAP by combining a fluorescently labeled recombinant 12-subunit RNAP system with single-molecule FRET measurements. We measured and compared the distances across the DNA binding channel of the archaeal RNAP. Our results show that the transition of the closed to the open initiation complex, which occurs concomitant with DNA melting, is coordinated with an opening of the RNAP clamp that is stimulated by TFE. We show that the clamp in elongation complexes is modulated by the nontemplate strand and by the processivity factor Spt4/5, both of which stimulate transcription processivity. Taken together, our results reveal an intricate network of interactions within transcription complexes between RNAP, transcription factors, and nucleic acids that allosterically modulate the RNAP during the transcription cycle.

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Faculty Opinions recommendation of Tunable and multifunctional eukaryotic transcription factors based on CRISPR/Cas.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.718106464.793483631 ◽

2013 ◽

Author(s):

D John Doyle ◽

Joseph Morgan MD

Keyword(s):

Transcription Factors ◽

Eukaryotic Transcription

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Second-site long terminal repeat (LTR) revertants of replication-defective human immunodeficiency virus: effects of revertant TATA box motifs on virus infectivity, LTR-directed expression, in vitro RNA synthesis, and binding of basal transcription factors TFIID and TFIIA.

Journal of Virology ◽

10.1128/jvi.68.5.3298-3307.1994 ◽

1994 ◽

Vol 68 (5) ◽

pp. 3298-3307 ◽

Cited By ~ 23

Author(s):

F Kashanchi ◽

R Shibata ◽

E K Ross ◽

J N Brady ◽

M A Martin

Keyword(s):

Human Immunodeficiency Virus ◽

Transcription Factors ◽

Long Terminal Repeat ◽

Rna Synthesis ◽

Tata Box ◽

Virus Infectivity ◽

Basal Transcription ◽

Immunodeficiency Virus ◽

Basal Transcription Factors

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Protein synthesis in yeast. Isolation of variant forms of elongation factor 1 from the yeast Saccharomyces cerevisiae.

Journal of Biological Chemistry ◽

10.1016/s0021-9258(18)67132-7 ◽

1986 ◽

Vol 261 (27) ◽

pp. 12599-12603

Author(s):

S K Saha ◽

K Chakraburtty

Keyword(s):

Saccharomyces Cerevisiae ◽

Protein Synthesis ◽

Elongation Factor ◽

Yeast Saccharomyces Cerevisiae ◽

Yeast Isolation ◽

Elongation Factor 1

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Selection of reference genes for gene expression analysis in Liriodendron hybrids’ somatic embryogenesis and germinative tissues

Scientific Reports ◽

10.1038/s41598-021-84518-w ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Tingting Li ◽

Weigao Yuan ◽

Shuai Qiu ◽

Jisen Shi

Keyword(s):

Gene Expression ◽

Somatic Embryogenesis ◽

Reference Genes ◽

Gene Selection ◽

Elongation Factor ◽

Reverse Transcription Pcr ◽

Expression Of Genes ◽

Suitable Reference ◽

Functional Analyses ◽

Elongation Factor 1

AbstractThe differential expression of genes is crucial for plant somatic embryogenesis (SE), and the accurate quantification of gene expression levels relies on choosing appropriate reference genes. To select the most suitable reference genes for SE studies, 10 commonly used reference genes were examined in synchronized somatic embryogenic and subsequent germinative cultures of Liriodendron hybrids by using quantitative real-time reverse transcription PCR. Four popular normalization algorithms: geNorm, NormFinder, Bestkeeper and Delta-Ct were used to select and validate the suitable reference genes. The results showed that elongation factor 1-gamma, histone H1 linker protein, glyceraldehyde-3-phosphate dehydrogenase and α-tubulin were suitable for SE tissues, while elongation factor 1-gamma and actin were best for the germinative organ tissues. Our work will benefit future studies of gene expression and functional analyses of SE in Liriodendron hybrids. It is also serves as a guide of reference gene selection in early embryonic gene expression analyses for other woody plant species.

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