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, 20 (11), 1932-9

Early Vertebrate Evolution of the TATA-binding Protein, TBP

Affiliations

Early Vertebrate Evolution of the TATA-binding Protein, TBP

Alla A Bondareva et al. Mol Biol Evol.

Abstract

TBP functions in transcription initiation in all eukaryotes and in Archaebacteria. Although the 181-amino acid (aa) carboxyl (C-) terminal core of the protein is highly conserved, TBP proteins from different phyla exhibit diverse sequences in their amino (N-) terminal region. In mice, the TBP N-terminus plays a role in protecting the placenta from maternal rejection; however the presence of similar TBP N-termini in nontherian tetrapods suggests that this domain also has more primitive functions. To gain insights into the pretherian functions of the N-terminus, we investigated its phylogenetic distribution. TBP cDNAs were isolated from representative nontetrapod jawed vertebrates (zebrafish and shark), from more primitive jawless vertebrates (lamprey and hagfish), and from a prevertebrate cephalochordate (amphioxus). Results showed that the tetrapod N-terminus likely arose coincident with the earliest vertebrates. The primary structures of vertebrate N-termini indicates that, historically, this domain has undergone events involving intragenic duplication and modification of short oligopeptide-encoding DNA sequences, which might have provided a mechanism of de novo evolution of this polypeptide.

Figures

Fig. 1
Fig. 1
Chordate TBPs. (a) Linear depiction of vertebrate TBP with domains indicated by different shading. (b) a.a. sequences of TBP proteins, with shaded bars above corresponding to the regions indicated in (a). Dots represent amino acids that are identical to the mouse sequence; gaps in alignment are exhibited by gaps in the presentation. The longer amphioxus N terminus is shown with the two extra a.a. underlined. For hagfish, variants containing 11, 12, and 13 Qs in the Q domain were isolated; 12 Qs are shown. (c) Oligonucleotide insertion-based polymorphisms in the aTBP 3′ UTR. Sequences for the three 3′-UTR mRNA isoforms that we identified are shown beginning at the stop codon (underlined). Nucleic acid positions for isoform number 1 are shown above the sequence in parentheses.
Fig. 2
Fig. 2
Predicted phylogeny of TBP N-termini (a) and C-termini (b). Relatedness is depicted as trees, with the p-distance scale indicated below each tree. The N-terminal sequences for B. floridae, D. melanogaster, and C. elegans cannot be reliably aligned with each other or with vertebrate TBP sequences, and thus these branches do not connect to the vertebrate tree or with each other (a) (see Materials and Methods). We find no evidence that the N-termini from these four groups are ancestrally related. Conversely, the C-terminal sequences are all homologous and an interconnected rooted tree is depicted (b).
Fig. 3
Fig. 3
Intron/exon structure of TBP N-terminus. (a) Southern blot of hagfish genomic DNA using a probe to the Q/NC region. Sequence analysis of partial cDNA clones indicated the presence of Eco RI (R1), Hind III (H3), and Pst I (P1) sites in the 5′end of C-terminus–encoding sequences. The upstream portion of the 6.7-kb Hind III fragment (second lane) was cloned by ligation-mediated PCR, revealing an unexpected intron interrupting the NC region of the gene. (b) Distribution of intron C. Primers were designed to amplify across this novel splice junction from all vertebrates (E.s., hagfish; P.m., lamprey; D.r., zebrafish; M.m., mouse). Amplification of cDNA samples (lanes labeled “c”) confirmed that the primers worked in all species. Amplification of genomic DNA (“g”) showed a larger product in hagfish and lamprey (asterisks), indicating the region contained an intron in these species. λ, HindIII/EcoRI-cut λ-DNA markers; p, HinfI-cut pBS+ markers. (c) Genomic DNA and amino acid sequence of the junction region. Intron sequences in lowercase font.
Fig. 4
Fig. 4
Transitions in the tbp gene during vertebrate phylogeny. At left is a diagram of vertebrate evolution based on published reports (Janvier 1999; Neidert et al. 2001; Delarbre et al. 2002). At right is a list of major modifications found in the structure or function of TBP, with the numbers corresponding to the indicated points on the diagram at left.
Fig. 5
Fig. 5
Models of minisatellite-dependent, oligopeptide-encoding sequence duplications. (a) Reading-frame independent preservation of amino acid sequences. A 7-aa region of the mouse NN region (top) was chosen as a starting sequence; however similar results are obtained with most arbitrary sequences (not shown). Twelve–base pair minisatellite duplications were modeled starting at each of eight consecutive nucleotides. Duplicated nucleotides are designated by bold font and underlining. Duplicated amino acids are underlined; novel amino acids are in bold. Few duplications (two of eight depicted) yield a novel amino acid, and this only occurs at the template/copy junction. (b) Within repeats, duplications preserve repeat periodicity. Model shows duplication of a 7-aa motif, “ABCDEFG” (21-bp minisatellite). Bold and underline indicate duplicated regions. Secondary duplications that initiate either at the first amino acid within the repeat (residue A, “in-step”) or at any other amino acid within the repeat (residues D and G shown, “out-of-step”) lead to the same trimeric repeat: ABCDEFGABCDEFGABCDEFG. The models in (a) and (b) show that imprecise or arbitrary duplications, as long as they occur in multiples of 3 bp, will tend to reiterate existing amino acid sequences and repeat motifs, rather than to insert novel amino acids or disrupt repeat units.

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