Index of papers in PLOS Comp. Biol. that mention
  • eukaryotic
Katja N. Rybakova, Frank J. Bruggeman, Aleksandra Tomaszewska, Martijn J. Moné, Carsten Carlberg, Hans V. Westerhoff
Abstract
Activation of eukaryotic transcription is an intricate process that relies on a multitude of regulatory proteins forming complexes on chromatin.
Author Summary
Such bursting transcriptional activity has indeed been observed for eukaryotic genes.
Discussion
In this study, we asked how transcription regulation of conditionally active genes in eukaryotes could be organized so that it is both fast enough, given diffusion limitations, and sensitive enough towards a large number of TFs.
Discussion
If one were to specify that histone modification is the process that marks the completion of a step in the multi-step process and sensitizes the local chromatin region for the assembly of the next protein complex, this model comes close to the accepted view of transcription activation in eukaryotes [7, 10, 22, 44].
Experimental evidence for the ticking mechanism
The ticking mechanism described above is consistent with the wealth of experimental evidence on the role of chromatin covalent-modification and remodelling in regulation of eukaryotic gene transcription [3, 5—7, 9, 10, 22, 44].
Introduction
Eukaryotic transcription depends on dozens of proteins, including transcription factors (TFs), chromatin remodellers and RNA polymerase II components [1—7].
Introduction
Even though we refer by ‘transcription regulation’ only to regulation of the transcription process itself and not to the regulation of gene expression through transcription, the complexity of eukaryotic transcription regulation is immense.
Number of proteins in a complex, n
This finding is highly relevant as the number of TF-binding sites actively regulating many eukaryotic genes is readily around ten or more.
Number of proteins in a complex, n
We will further discuss alternative mechanisms for eukaryotic gene regulation that do not suffer from this limitation.
Reversible assembly of large protein complexes can take tens of minutes
In summary, our analysis indicates that for many eukaryotic genes mechanism of reversible association of all TFs becomes too slow.
Revertibility of transcription activation requires a cycle
Our analysis thus far has used criteria of regulatory sensitivity and the speed of regulation of transcription to show that a ‘ticking’ transcription cycle mechanism is an attractive mechanism for eukaryotic genes that are regulated by multiple TFs.
eukaryotic is mentioned in 19 sentences in this paper.
Topics mentioned in this paper:
Thomas W. Spiesser, Clemens Kühn, Marcus Krantz, Edda Klipp
Author Summary
Our analysis shows how the nature of the two linked properties growth and proliferation can shape eukaryotic cells and eXplain cell size as an emergent rather than regulatory property of this process.
Introduction
The unicellular eukaryote Saccharomyces cerevisiae can be observed to grow to a ‘critical cell size’ in the G1 phase before committing to passage through the cell cycle [1].
Results
We present here an extended version of a minimal eukaryotic cell model that is capable of growth and division (Fig 1A) [32].
The model
The model is an extension of a minimal eukaryotic cell model [32].
The model
The cell cycle of the model has four transitions, corresponding to the eukaryotic phase transitions (G 1/ S, S/GZ, Gz/M, M/ G1).
eukaryotic is mentioned in 5 sentences in this paper.
Topics mentioned in this paper:
Vesna Memišević, Nela Zavaljevski, Seesandra V. Rajagopala, Keehwan Kwon, Rembert Pieper, David DeShazer, Jaques Reifman, Anders Wallqvist
Abstract
Burkholderia pathogenicity relies on protein virulence factors to control and promote bacterial internalization, survival, and replication within eukaryotic host cells.
Author Summary
Burkholderia species need to manipulate many host processes and pathways in order to establish a successful intracellular infection in eukaryotic host organisms.
Introduction
This host-adapted bacterium is equipped with an extensive set of mechanisms for invasion and modulation of eukaryotic host-cell environments.
Summary
Using multiple virulence factors to target eukaryotic-specific mechanisms common to eukaryotic rhizosphere species, B. mallei broadly influences key processes in ubiquitination and cell signaling to modulate and adapt the host-cell environment for its benefit.
eukaryotic is mentioned in 4 sentences in this paper.
Topics mentioned in this paper: