Archaeal Transcription

Overview

Journal Transcription

Specialty Molecular Biology

Date 2020 Oct 28

PMID 33112729

Citations 8

Authors

Breanna R Wenck

Thomas J Santangelo

Affiliations

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Abstract

Increasingly sophisticated biochemical and genetic techniques are unraveling the regulatory factors and mechanisms that control gene expression in the Archaea. While some similarities in regulatory strategies are universal, archaeal-specific regulatory strategies are emerging to complement a complex patchwork of shared archaeal-bacterial and archaeal-eukaryotic regulatory mechanisms employed in the archaeal domain. The prokaryotic archaea encode core transcription components with homology to the eukaryotic transcription apparatus and also share a simplified eukaryotic-like initiation mechanism, but also deploy tactics common to bacterial systems to regulate promoter usage and influence elongation-termination decisions. We review the recently established complete archaeal transcription cycle, highlight recent findings of the archaeal transcription community and detail the expanding post-initiation regulation imposed on archaeal transcription.

Citing Articles

High hydrostatic pressure promotes gene transcription via a cystathionine-β-synthase domain-containing protein in the hyperthermophilic archaeon Pyrococcus yayanosii.

Li C, Li S, Song Q, Da L, Xu J Nucleic Acids Res. 2025; 53(1.

PMID: 39777464 PMC: 11705074. DOI: 10.1093/nar/gkae1289.

Sequencing-based analysis of microbiomes.

Pinto Y, Bhatt A Nat Rev Genet. 2024; 25(12):829-845.

PMID: 38918544 DOI: 10.1038/s41576-024-00746-6.

The Archaeal Cell Cycle.

Cezanne A, Foo S, Kuo Y, Baum B Annu Rev Cell Dev Biol. 2024; 40(1):1-23.

PMID: 38748857 PMC: 7617429. DOI: 10.1146/annurev-cellbio-111822-120242.

Archaeal histone-based chromatin structures regulate transcription elongation rates.

Wenck B, Vickerman R, Burkhart B, Santangelo T Commun Biol. 2024; 7(1):236.

PMID: 38413771 PMC: 10899632. DOI: 10.1038/s42003-024-05928-w.

Putative nucleotide-based second messengers in archaea.

van der Does C, Braun F, Ren H, Albers S Microlife. 2023; 4:uqad027.

PMID: 37305433 PMC: 10249747. DOI: 10.1093/femsml/uqad027.

References

Takemata N, Samson R, Bell S . Physical and Functional Compartmentalization of Archaeal Chromosomes. Cell. 2019; 179(1):165-179.e18. PMC: 6756186. DOI: 10.1016/j.cell.2019.08.036. View

Deighan P, Hochschild A . Conformational toggle triggers a modulator of RNA polymerase activity. Trends Biochem Sci. 2006; 31(8):424-6. DOI: 10.1016/j.tibs.2006.06.004. View

Le T, Yang Y, Tan C, Suhanovsky M, Fulbright Jr R, Inman J . Mfd Dynamically Regulates Transcription via a Release and Catch-Up Mechanism. Cell. 2017; 172(1-2):344-357.e15. PMC: 5766421. DOI: 10.1016/j.cell.2017.11.017. View

Jun S, Hirata A, Kanai T, Santangelo T, Imanaka T, Murakami K . The X-ray crystal structure of the euryarchaeal RNA polymerase in an open-clamp configuration. Nat Commun. 2014; 5:5132. PMC: 4657547. DOI: 10.1038/ncomms6132. View

Kanai T, Akerboom J, Takedomi S, van de Werken H, Blombach F, van der Oost J . A global transcriptional regulator in Thermococcus kodakaraensis controls the expression levels of both glycolytic and gluconeogenic enzyme-encoding genes. J Biol Chem. 2007; 282(46):33659-33670. DOI: 10.1074/jbc.M703424200. View

Bintrim S, Donohue T, Handelsman J, Roberts G, Goodman R . Molecular phylogeny of Archaea from soil. Proc Natl Acad Sci U S A. 1997; 94(1):277-82. PMC: 19314. DOI: 10.1073/pnas.94.1.277. View

Murakami K . Structural biology of bacterial RNA polymerase. Biomolecules. 2015; 5(2):848-64. PMC: 4496699. DOI: 10.3390/biom5020848. View

Blombach F, Smollett K, Grohmann D, Werner F . Molecular Mechanisms of Transcription Initiation-Structure, Function, and Evolution of TFE/TFIIE-Like Factors and Open Complex Formation. J Mol Biol. 2016; 428(12):2592-2606. PMC: 7616663. DOI: 10.1016/j.jmb.2016.04.016. View

Bell S, Brinkman A, van der Oost J, Jackson S . The archaeal TFIIEalpha homologue facilitates transcription initiation by enhancing TATA-box recognition. EMBO Rep. 2001; 2(2):133-8. PMC: 1083817. DOI: 10.1093/embo-reports/kve021. View

10.

Yue L, Li J, Zhang B, Qi L, Li Z, Zhao F . The conserved ribonuclease aCPSF1 triggers genome-wide transcription termination of Archaea via a 3'-end cleavage mode. Nucleic Acids Res. 2020; 48(17):9589-9605. PMC: 7515710. DOI: 10.1093/nar/gkaa702. View

11.

Krell T . Exploring the (Almost) Unknown: Archaeal Two-Component Systems. J Bacteriol. 2018; 200(7). PMC: 5847645. DOI: 10.1128/JB.00774-17. View

12.

Darnell C, Zheng J, Wilson S, Bertoli R, Bisson-Filho A, Garner E . The Ribbon-Helix-Helix Domain Protein CdrS Regulates the Tubulin Homolog To Control Cell Division in Archaea. mBio. 2020; 11(4). PMC: 7439475. DOI: 10.1128/mBio.01007-20. View

13.

Lemmens L, Ramadan Maklad H, Bervoets I, Peeters E . Transcription Regulators in Archaea: Homologies and Differences with Bacterial Regulators. J Mol Biol. 2019; 431(20):4132-4146. DOI: 10.1016/j.jmb.2019.05.045. View

14.

Fouqueau T, Blombach F, Hartman R, Cheung A, Young M, Werner F . The transcript cleavage factor paralogue TFS4 is a potent RNA polymerase inhibitor. Nat Commun. 2017; 8(1):1914. PMC: 5715097. DOI: 10.1038/s41467-017-02081-3. View

15.

Maier L, Marchfelder A . It's all about the T: transcription termination in archaea. Biochem Soc Trans. 2019; 47(1):461-468. DOI: 10.1042/BST20180557. View

16.

Lawson M, Ma W, Bellecourt M, Artsimovitch I, Martin A, Landick R . Mechanism for the Regulated Control of Bacterial Transcription Termination by a Universal Adaptor Protein. Mol Cell. 2018; 71(6):911-922.e4. PMC: 6151137. DOI: 10.1016/j.molcel.2018.07.014. View

17.

French S, Santangelo T, Beyer A, Reeve J . Transcription and translation are coupled in Archaea. Mol Biol Evol. 2007; 24(4):893-5. DOI: 10.1093/molbev/msm007. View

18.

Decker K, Hinton D . Transcription regulation at the core: similarities among bacterial, archaeal, and eukaryotic RNA polymerases. Annu Rev Microbiol. 2013; 67:113-39. DOI: 10.1146/annurev-micro-092412-155756. View

19.

HAUSNER W, Lange U, Musfeldt M . Transcription factor S, a cleavage induction factor of the archaeal RNA polymerase. J Biol Chem. 2000; 275(17):12393-9. DOI: 10.1074/jbc.275.17.12393. View

20.

Korkhin Y, Unligil U, Littlefield O, Nelson P, Stuart D, Sigler P . Evolution of complex RNA polymerases: the complete archaeal RNA polymerase structure. PLoS Biol. 2009; 7(5):e1000102. PMC: 2675907. DOI: 10.1371/journal.pbio.1000102. View