Same same but different: The evolution of TBP in archaea and their eukaryotic offspring

Blombach, Fabian; Grohmann, Dina

doi:10.1080/21541264.2017.1289879

Cited by 11 publications

(12 citation statements)

References 30 publications

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“…Transcription in all domains of life has to be fine-tuned over a wide range of synthesis rates that can respond to environmental cues. Compared to Bacteria as well as Eukaryotes (RNAP II), archaeal promoters show a lower apparent complexity in terms of promoter element composition 33,34 . What we know thus far is that archaeal transcription is regulated via enhancing or impairing the recruitment of PICs to the promoter 37–40 .…”

Section: Discussionmentioning

confidence: 99%

“…Archaeal promoters seem to comprise fewer promoter elements compared to their bacterial and eukaryotic counterparts, but it is possible that additional unknown sequence elements as well as the physicochemical properties of promoter DNA contribute to promoter strength 33,34 . Likewise, our understanding of transcription regulation is limited to factors modulating the recruitment of PICs 35,36 where repression generally involves steric hindrance of RNAP or basal initiation factor binding and activation is achieved by enhancing their binding 37–40 .…”

Section: Introductionmentioning

confidence: 99%

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Promoter-proximal elongation regulates transcription in archaea

Blombach

Fouqueau

Matelska

et al. 2020

Preprint

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Recruitment of RNA polymerase and initiation factors to the promoter is the only known mechanisms for transcription activation and repression in archaea. Whether any of the subsequent steps towards productive transcription elongation is involved in regulation is not known. We characterised how the basal transcription machinery is distributed along genes in the archaeon Sulfolobus solfataricus. We discovered a distinct early elongation phase where RNA polymerases sequentially recruit the elongation factors Spt4/5 and Elf1 to form the transcription elongation complex (TEC) before the TEC escapes into productive transcription. TEC escape is rate-limiting for transcription output during exponential growth. Oxidative stress causes changes in TEC escape that correlate with changes in the transcriptome. Our results thus establish that TEC escape contributes to the basal promoter strength and facilitates transcription regulation. Impaired TEC escape coincides with the accumulation of initiation factors at the promoter and recruitment of termination factor aCPSF1 to the early TEC. This suggests two possible mechanisms for how TEC escape limits transcription, physically blocking upstream RNA polymerases during transcription initiation and premature termination of early TECs.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Promoter-proximal elongation regulates transcription in archaea

Blombach

Fouqueau

Matelska

et al. 2020

Preprint

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“…TATA box and BRE are DNA sequence recognition motifs of the two general transcription factors TBP and TFB, respectively (Bell et al 1999;Qureshi et al 1995;Rowlands et al 1994), both TBP and TFB are necessary and sufficient to facilitate promoter-directed transcription in vitro (Werner and Weinzierl 2002). TBP and TFB are homologous to eukaryotic TBP and TFIIB, respectively, and have identical functions, albeit with a faster DNA-binding dynamics (Gietl et al 2014) that may reflect different mechanisms of regulation (Blombach and Grohmann 2017). Global mapping of transcription start sites (TSSs) and subsequent Chapter 5 promoter sequence analysis confirm in vitro observations in as much as TATA and BRE motifs are dominant elements in most archaeal promoters, with a few notable exceptions including the M. jannaschii ribosomal RNA promoter (Fig 1.3, Fig.…”

Section: Promoter Recognition and Recruitment Of The Rnapmentioning

confidence: 99%

A Global Characterisation of the Archaeal Transcription Machinery

Smollett

Blombach

Fouqueau

et al. 2017

RNA Metabolism and Gene Expression in Archaea

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Archaea employ a eukaryote-like transcription apparatus to transcribe a bacteria-like genome; while the RNA polymerase, basal factors and promoter elements mirror the eukaryotic RNA polymerase II system, archaeal genomes are densely packed with genes organised into multicistronic transcription units. The molecular mechanisms of archaeal transcription have been studied and characterised in great detail in vitro, but until recently relatively little was known about its global characteristics. In this chapter we discuss an integrated view of transcription from the molecular to the global level. Systems biology approaches have provided compelling insights into promoter and terminator DNA elements, the genome-wide distribution of transcription initiation-and elongation factors and RNA polymerase, the archaeal transcriptome and chromatin organisation. Overall these analyses illuminate transcription from a genome-wide perspective and serve as a resource for the community. In addition, Big Data can often validate mechanistic models based on biochemical and structural information, and generate new working hypotheses that can be thoroughly tested and dissected in vitro. This is an exciting time to study gene expression in the archaea since we are at the brink of a comprehensive yet detailed understanding of transcription.

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“…TBP is highly conserved throughout Eukarya (8,9). The C-terminal DNA binding domain of TBP consisting of 181 amino acids can be found from Archaea to Humans (10)(11)(12). Indeed, TBP purified from…”

Section: Introductionmentioning

confidence: 99%

“…TBP is highly conserved throughout Eukarya (8, 9). The C-terminal DNA binding domain of TBP consisting of 181 amino acids can be found from Archaea to Humans (10–12). Indeed, TBP purified from Saccharomyces cerevisiae can substitute for mammalian TFIID in in vitro transcription systems (13, 14).…”

Section: Introductionmentioning

confidence: 99%

A TBP-independent mechanism for RNA Polymerase II transcription

Budzyński

et al. 2021

Preprint

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Transcription by RNA Polymerase II (Pol II) is initiated by the hierarchical assembly of the Pre-Initiation Complex onto promoter DNA. Decades of in vitro and yeast research have shown that the TATA-box binding protein (TBP) is essential to Pol II initiation by triggering the binding of other general transcription factors, and ensuring proper Pol II loading. Here, we report instead that acute depletion of TBP in mouse embryonic stem cells (mESCs) has no global effect on ongoing Pol II transcription. Surprisingly, Pol II transcriptional induction through the Heat Shock Response or cellular differentiation also occurs normally in the absence of TBP. In contrast, acute TBP depletion severely impairs initiation by RNA Polymerase III. Lastly, we show that a metazoan-specific paralog of TBP is expressed in mESCs and that it binds to promoter regions of active Pol II genes even in the absence of TBP. Taken together, our findings reveal an unexplored TBP-independent process in mESCs that points to a diversity in Pol II transcription initiation mechanisms.

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Same same but different: The evolution of TBP in archaea and their eukaryotic offspring

Cited by 11 publications

References 30 publications

Promoter-proximal elongation regulates transcription in archaea

Promoter-proximal elongation regulates transcription in archaea

A Global Characterisation of the Archaeal Transcription Machinery

A TBP-independent mechanism for RNA Polymerase II transcription

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