title: A model for genesis of transcription systems.
abstract: 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., (-12)TATAATG(-6)) so closely resemble TATA boxes (i.e., (-31)TATAAAAG(-24)) in archaeal/eukaryotic transcription. The evolution of anchor DNA sequences in bacterial (i.e., (-35)TTGACA(-30)) and archaeal (BRE(up); BRE for TFB recognition element) promoters is potentially explained. The evolution of BRE(down) elements of archaeal promoters is potentially explained.
authors.affiliation: a Department of Biochemistry and Molecular Biology , Michigan State University , E. Lansing , MI , USA.
authors.forename: Zachary F
authors.initials: ZF
authors.lastname: Burton
authors.affiliation: b Department of Mathematics , Michigan State University , E. Lansing , MI , USA.
authors.forename: Kristopher
authors.initials: K
authors.lastname: Opron
authors.affiliation: b Department of Mathematics , Michigan State University , E. Lansing , MI , USA.
authors.forename: Guowei
authors.initials: G
authors.lastname: Wei
authors.affiliation: c Department of Chemistry , Michigan State University , E. Lansing , MI , USA.
authors.forename: James H
authors.initials: JH
authors.lastname: Geiger
mesh_terms: D019843:Archaeal Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D001426:Bacterial Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D001665:Binding Sites; D012321:DNA-Directed RNA Polymerases / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D019143:Evolution, Molecular; D008958:Models, Molecular; D011401:Promoter Regions, Genetic; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D018741:Replication Origin; D014157:Transcription Factors / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D014158:Transcription, Genetic
chemical_list: D019843:Archaeal Proteins; D001426:Bacterial Proteins; D014157:Transcription Factors; D012321:DNA-Directed RNA Polymerases
keywords: LECA (the last eukaryotic common ancestor); LUCA (the last universal common cellular ancestor); RIFT barrels; RNA polymerase; Rossmann folds; TATA-binding protein (TBP); TIM barrels; cradle-loop barrel metafold; double-Ψ−β-barrels; general transcription factors; replication; the carboxy terminal domain (CTD) of RNA polymerase II; transcription; transcription factor B (TFB); α/β protein folds; σ factors