The σ enigma: Bacterial σ factors, archaeal TFB and eukaryotic TFIIB are homologs

Burton, Samuel P; Burton, Zachary F.

doi:10.4161/21541264.2014.967599

Cited by 38 publications

(44 citation statements)

References 33 publications

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“…Bacterial sigma transcription factors are homologs of archaeal TFB and evolved from a ≥four helix-turn-helix repeat. 16 , 17 Archaeal and bacterial promoters are posited to be evolved from a ≥(TFB-recognition element-TATA box) 4 repeat, initially recognized by a ≥(helix-turn-helix) 4 repeat primordial initiation factor (a precursor of archaeal TFB and bacterial sigma) and also TBP. 16 The carboxy terminal domain of eukaryotic RNA polymerase II is a (YSPTSPS) n repeat.…”

Section: Discussionmentioning

confidence: 99%

tRNA structure and evolution and standardization to the three nucleotide genetic code

2017

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Cloverleaf tRNA with a 75 nucleotide (nt) core is posited to have evolved from ligation of three 31 nt minihelices followed by symmetric internal deletions of 9 nt within ligated acceptor stems. Statistical tests strongly support the model. Although the tRNA anticodon loop and T loop are homologs, their U-turns have been treated as distinct motifs. An appropriate comparison, however, shows that intercalation of D loop G19 between T loop bases 4 and 5 causes elevation of T loop base 5 and flipping of T loop bases 6 and 7 out of the 7 nt loop. In the anticodon loop, by contrast, loop bases 3–7 stack tightly to form a stiff connection to mRNA. Furthermore, we identify ancient repeat sequences of 3 (GCG), 5 (UAGCC) and 17 nt (∼CCGGGUUCAAAACCCGG) that comprise 75 out of 75 nts of the tRNA cloverleaf core. To present a sufficiently stiff 3-nt anticodon, a 7-nt anticodon loop was necessary with a U-turn between loop positions 2 and 3. Cloverleaf tRNA, therefore, was a radical evolutionary innovation essential for the 3-nt code. Conservation of GCG and UAGCC repeat sequences indicates that cloverleaf tRNA is at the interface between a strange RNA repeat world and the first evolution of molecules that fold to assume biologic functions. We posit that cloverleaf tRNA was the molecular archetype around which translation systems evolved.

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Section: Discussionmentioning

confidence: 99%

tRNA structure and evolution and standardization to the three nucleotide genetic code

2017

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“…Here we describe evolution of TBP (TATA-binding protein) and a primordial transcription initiation factor that gave rise to σ factors in bacteria and to TFB (Transcription Factor B) in archaea, driving divergence of bacteria and archaea. 35 TBP includes 2 TBP-fold repeats. TFB, with 2-HTH (helix-turn-helix) repeats, appears to be derived from a 4-HTH primordial initiation factor.…”

Section: A Simple Model For Evolution Of Rnaps General Transcriptionmentioning

confidence: 99%

“…Both TBP and the 4-HTH primordial initiation factor are posited to have existed at LUCA. 35 As described above, at LUCA, GTFs can also be considered replication origin binding factors, because replication on the first DNA templates initiated via transcription followed by reverse transcription. 7 TBP was generated via duplication of a TBP fold, and, consistent with its near 2-fold symmetry, TBP lands within the DNA minor groove at the TATAAAAG box.…”

Section: A Simple Model For Evolution Of Rnaps General Transcriptionmentioning

confidence: 99%

“…Bacterial σ factors are derived from a repeat of 4-HTH domains, but, because of coevolution with RNAP and promoters, the 4-HTH repeat structure in σ, although recognizable, is degenerate in sequence. 35

Figure 4. A model for evolution of bacterial σ factors and archaeal TFB from a 4-HTH primordial initiation factor at LUCA.…”

Section: A Simple Model For Evolution Of Rnaps General Transcriptionmentioning

confidence: 99%

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A model for genesis of transcription systems

et al. 2016

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Repeating sequences generated from RNA gene fusions/ligations dominate ancient life, indicating central importance of building structural complexity in evolving biological systems. A simple and coherent story of life on earth is told from tracking repeating motifs that generate α/β proteins, 2-double-Ψ−β-barrel (DPBB) type RNA polymerases (RNAPs), general transcription factors (GTFs), and promoters. A general rule that emerges is that biological complexity that arises through generation of repeats is often bounded by solubility and closure (i.e., to form a pseudo-dimer or a barrel). Because the first DNA genomes were replicated by DNA template-dependent RNA synthesis followed by RNA template-dependent DNA synthesis via reverse transcriptase, the first DNA replication origins were initially 2-DPBB type RNAP promoters. A simplifying model for evolution of promoters/replication origins via repetition of core promoter elements is proposed. The model can explain why Pribnow boxes in bacterial transcription (i.e., −12TATAATG−6) so closely resemble TATA boxes (i.e., −31TATAAAAG−24) in archaeal/eukaryotic transcription. The evolution of anchor DNA sequences in bacterial (i.e., −35TTGACA−30) and archaeal (BREup; BRE for TFB recognition element) promoters is potentially explained. The evolution of BREdown elements of archaeal promoters is potentially explained.

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“…TFB is able to recognize the TBP-DNA complex, binds to it and recruits the RNAP yielding the pre-initiation complex (PIC) [16]. TFB is composed of the zinc ribbon (ZR) and the C-terminal core domain, which are connected by a flexible linker [17,18]. The core domain contacts the B-recognition element located upstream of the TATA box in the promoter DNA and spans across the DNA-binding channel.…”

Section: Introductionmentioning

confidence: 99%

Fluorescently labeled recombinant RNAP system to probe archaeal transcription initiation

Schulz

Kramm

Werner

et al. 2015

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The σ enigma: Bacterial σ factors, archaeal TFB and eukaryotic TFIIB are homologs

Cited by 38 publications

References 33 publications

tRNA structure and evolution and standardization to the three nucleotide genetic code

tRNA structure and evolution and standardization to the three nucleotide genetic code

A model for genesis of transcription systems

Fluorescently labeled recombinant RNAP system to probe archaeal transcription initiation

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