Structure and mechanisms of viral transcription factors in archaea

Sheppard, Carol; Werner, Finn

doi:10.1007/s00792-017-0951-1

Cited by 14 publications

(12 citation statements)

References 71 publications

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“…In Archaea, cooperative lateral spreading of filaments has been reported for Alba proteins [ 40 , 42 , 119 , 120 ]. Also, promoter occlusion mechanisms and competitive binding of archaeal NAPs and transcription factors have been reported [ 45 , 121 , 122 ].…”

Section: Histones Are Found In Some Newly Discovered Archaeamentioning

confidence: 99%

Structure and function of archaeal histones

et al. 2018

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The genomes of all organisms throughout the tree of life are compacted and organized in chromatin by association of chromatin proteins. Eukaryotic genomes encode histones, which are assembled on the genome into octamers, yielding nucleosomes. Post-translational modifications of the histones, which occur mostly on their N-terminal tails, define the functional state of chromatin. Like eukaryotes, most archaeal genomes encode histones, which are believed to be involved in the compaction and organization of their genomes. Instead of discrete multimers, in vivo data suggest assembly of “nucleosomes” of variable size, consisting of multiples of dimers, which are able to induce repression of transcription. Based on these data and a model derived from X-ray crystallography, it was recently proposed that archaeal histones assemble on DNA into “endless” hypernucleosomes. In this review, we discuss the amino acid determinants of hypernucleosome formation and highlight differences with the canonical eukaryotic octamer. We identify archaeal histones differing from the consensus, which are expected to be unable to assemble into hypernucleosomes. Finally, we identify atypical archaeal histones with short N- or C-terminal extensions and C-terminal tails similar to the tails of eukaryotic histones, which are subject to post-translational modification. Based on the expected characteristics of these archaeal histones, we discuss possibilities of involvement of histones in archaeal transcription regulation.

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Section: Histones Are Found In Some Newly Discovered Archaeamentioning

confidence: 99%

Structure and function of archaeal histones

et al. 2018

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“…At higher regulator concentrations, RHH proteins begin to oligomerize along DNA towards the core promoter, leading to the occupation of degenerate (low-affinity) binding sites and subsequent activation. In other cases, the process is accompanied by repression when oligomers presumably interfere with preinitiation complex (PIC) assembly [ 165 , 166 ].…”

Section: Mechanisms Of Transcription Activation In Archaeamentioning

confidence: 99%

Evolution of Regulated Transcription

Bylino

Ibragimov

Shidlovskii

2020

Cells

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The genomes of all organisms abound with various cis-regulatory elements, which control gene activity. Transcriptional enhancers are a key group of such elements in eukaryotes and are DNA regions that form physical contacts with gene promoters and precisely orchestrate gene expression programs. Here, we follow gradual evolution of this regulatory system and discuss its features in different organisms. In eubacteria, an enhancer-like element is often a single regulatory element, is usually proximal to the core promoter, and is occupied by one or a few activators. Activation of gene expression in archaea is accompanied by the recruitment of an activator to several enhancer-like sites in the upstream promoter region. In eukaryotes, activation of expression is accompanied by the recruitment of activators to multiple enhancers, which may be distant from the core promoter, and the activators act through coactivators. The role of the general DNA architecture in transcription control increases in evolution. As a whole, it can be seen that enhancers of multicellular eukaryotes evolved from the corresponding prototypic enhancer-like regulatory elements with the gradually increasing genome size of organisms.

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“…mechanisms of the archaeal hosts is provided by CRISPR-Cas systems [97]. Sophisticated viral counter measures involve the subjugation of the host transcription machineries, as well as strategies to stay 'under the radar' of surveillance mechanisms including the type IIIb CRISPR-Cas system that is triggered by active transcription [98][99][100]. Encounters between the Acidianus two-tailed virus (ATV) and S. solfataricus are witnessed by the presence of several ATV genome-derived CRISPR spacers in the hosts' CRISPR arrays, including sequences mapping to a small gene called ORF145 [101].…”

Section: Global Inhibition Of Transcription In the Host-virus Arms Racementioning

confidence: 99%

The cutting edge of archaeal transcription

Fouqueau

Blombach

Cackett

et al. 2018

Emerging Topics in Life Sciences

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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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Structure and mechanisms of viral transcription factors in archaea

Cited by 14 publications

References 71 publications

Structure and function of archaeal histones

Structure and function of archaeal histones

Evolution of Regulated Transcription

The cutting edge of archaeal transcription

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