Bs1, a new chimeric gene formed by retrotransposon-mediated exon shuffling in maize

Abstract

Transposons are major components of all eukaryotic genomes. Although traditionally regarded as causes of detrimental mutations, recent evidence suggests that transposons may play a role in host gene diversification and evolution. For example, host gene transduction by retroelements has been suggested to be both common and to have the potential to create new chimeric genes by the shuffling of existing sequences. We have previously shown that the maize (Zea mays subsp. mays) retrotransposon Bs1 has transduced sequences from three different host genes. Here, we provide evidence that these transduction events led to the generation of a chimeric new gene that is both transcribed and translated. Expression of Bs1 is tightly controlled and occurs during a narrow developmental window in early ear development. Although all Bs1-associated transduction events took place before Zea speciation, a full uninterrupted open reading frame encoding the BS1 protein may have arisen in domesticated maize or in the diverse populations of its progenitor Z. mays subsp. parviglumis. We discuss potential functions based on domain conservation and evidence for functional constraints between the transduced sequences and their host gene counterparts.

Figure 1.

Bs1 is expressed in reproductive tissues. A, RT-PCR analysis of Bs1 mRNA extracted from Z. mays subsp. mays. Lanes 1 and 16 contain a M_r marker. Lanes 2 to 8 contain young ear (stage R1 or early stage R2, when silk starts to be visible outside the husks [Hanway and Ritchie 1984]; W22), young ear (Oh43), young tassel (W22), young tassel (Oh43), husk (Oh43), silk-free ear (Oh43), and silk (Oh43), respectively. Lanes 9 to 12 contain Oh43 root, 1-week-old seedling, 2-week-old seedling leaf, and mature leaf, respectively. Lanes 13 to 15 contain controls in which reverse transcriptase was omitted during first-strand cDNA synthesis; lane 13 contains young ear (Oh43), lane 14 contains young ear (W22), and lane 15 contains young tassel (Oh43). B, RT-PCR analysis of Abp1 mRNA extracted from Z. mays subsp. mays (Oh43) using the primer pair shown in the schematic in C (represented by arrowheads). Lane 1 contains a M_r marker and lanes 2 to 8 contain young ear, young tassel, root, seedling leaf, 8-week-old leaf, silk, and husk, respectively. Lane 9 contains a PCR amplification product using the same primer pair used for RT-PCR but with genomic DNA as a template. C, Schematic depiction of the Abp1 gene showing primers (arrowheads) used in B. The primers used to amplify the Bs1 transcript are indicated by arrows above the Bs1 structure depicted in Figure 4.

Figure 2.

Bs1 is translated. Immunoblot analysis using total bacterial (A) or plant (B–E) extracts. In A, extracts from a bacterial strain containing a plasmid expressing the N-terminal 301 amino acids (lane 1) or the empty plasmid (lane 2) were probed with anti-BS1 antiserum. In B to D, extracts from young ears, sterile ears, or leaves (lanes 1–3, respectively) were probed with the anti-BS1 antiserum (B), preimmune serum (C), or anti-BS1 antiserum that had been incubated with a BS1 synthetic peptide (D). In E, proteins extracted from mature leaf, 2-week-old seedling leaf, 1-week-old seedling, silk, young ear, young tassel, endosperm, pericarp, and embryo (lanes 1–9, respectively) were probed with anti-BS1 antibody. In all panels, the left-most lane contains a M_r marker. [See online article for color version of this figure.]

Figure 3.

Bs1 is involved during normal reproductive development. A, Photograph of normal (right) and sterile (left) maize ears. B, Immunoblot analysis using anti-BS1 antibody and proteins extracted from leaf, normal young tassel, post-pollen tassel, leaf, normal young ear, and sterile ear (lanes 2–7, respectively). C, Immunoblot analysis using anti-ubiquitin antibody and protein extracts as in B. The brace indicates high molecular mass ubiquitinated proteins, and the arrow indicates free ubiquitin. Lane 1 contains a molecular mass marker with sizes in kilodaltons. [See online article for color version of this figure.]

Figure 4.

Structure and evolution of Bs1 in maize and the teosintes. Top, The Bs1 structure showing the three transduced genes (r-bg, r-xe, and r-pma), the gag and env domains, and the retroelement LTR. ORF1 and the hypothetical ORF2 are shown below. Primers used for RT-PCR are indicated by the arrows. Bottom, The different Bs1 copies in maize and the teosintes are represented by horizontal lines, deletions and insertions and their sizes in base pairs by triangles, and stop codons by asterisks.