Retrotransposons are a class of mobile DNA sequences in eukaryotes that transpose through a reverse-transcribed RNA intermediate. Retrotransposons containing long terminal repeats have many of the attributes of retroviruses in animals but have not been previously observed to acquire a portion of a cellular gene as RNA tumor viruses do with oncogenes. We have found homology to plasma membrane proton ATPase genes within the Bsl retrotransposon of maize, and this homology led us to clone the maize plasma membrane proton ATPase gene, which we have named Mhal. The sequence of Mhal confirmed that 654 bp of this ATPase gene are present in Bsl; this segment represents the last amino acid of exon 4, all of exons 5 to 9, and part of exon 10. All introns have been removed from this acquired DNA, whereas 81 single base pair substitutions and a deletion of 183 bp in Bsl differentiate these contiguous segments. The secondary mutations led to fewer changes in the derived Bsl protein sequence than predicted for neutra1 events, suggesting that the acquired Mhal DNA performs a selected function within Bsl. These data indicate that a retrotransposon can incorporate and transmit a portion of a standard nuclear gene transcript within its genetic material. Alternatively, these results suggest that Bsl may represent a defective version of a plant retrovirus.

We have sequenced Bs), an insertion element isolated from a null allele of the Adhi locus encoding alcohol dehydrogenase in maize. The Bs) element is 3203 base pairs (bp) in length, has 302-bp identical long terminal direct repeats (LTRs), and created a 5-bp flanking direct duplication oftarget AdhI DNA upon insertion. The 5' LTR is followed by a canonical primer binding site with homology to the plant initiator methionyl-tRNA, and the 3' LTR is directly preceded by a polypurine stretch like that observed in retroviruses and retrotransposons. Bs) encodes two overlapping open reading frames specifying peptides of 740 and 168 amino acids. The longer open reading frame specifies a peptide with amino acid homology to the protease and nucleic acid binding moiety of retroviruses and retrotransposons. The deduced amino acid sequence encoded by Bsl lacks convincing homology to the polymerase (reverse transcriptase) encoded by retroposons, despite the fact that this polymerase-encoding domain is routinely the most conserved region of any such element. The sequence and relatively small size of Bs) suggest that this element is a deleted retrotransposon that inserted into AdhM with the aid of a reverse transcriptase function provided in trans. In vitro transcribed Bsl complementary RNA was translated in vitro to produce both a protein of 81 kDa representing open reading frame 1 (ORF1) and one of the 95-kDa size predicted for the frame-shifted fusion of ORF1 and ORF2. As with many other retroposons, the efficiency of translational initiation at the AUG beginning ORF1 was not noticeably affected by the presence of one or more upstream, unproductive AUGs in the complementary RNA transcript.By both structural and mechanistic criteria, eukaryotic insertion sequences and transposable elements can be divided into two major categories. One class of elements is bounded by inverted terminal repeat sequences and transposes through excision (1, 2) and/or enhanced replication (3) of the integrated element. Examples of this class of transposable elements are the controlling elements of maize (4) and the P elements of Drosophila (5). A second class of eukaryotic insertion sequences, the "retroposons," integrate into the chromosome after reverse transcription of element-encoded RNA (6), are particularly abundant in animals, and are the only type of insertion sequence yet discovered in fungi. Both the retroviruses (6) and the LI elements (7) of vertebrates and the "retrotransposons" Ty of yeast (8) and copia of Drosophila (9) fall into this latter category.Despite the early discovery and characterization of numerous distinct transposable elements in maize (1, 4), a canonical retrovirus or retrotransposon has not been described in plants. The DNA caulimoviruses ofplants have the structural properties and encode the reverse transcriptase activity definitional of a retrovirus or retrotransposon but apparently do not integrate into chromosomal DNA (10). Recently, Schwarz-Sommer et al. (11) have found that the Cin4 insertion element of m...

Retrotransposons are a class of mobile DNA sequences in eukaryotes that transpose through a reverse-transcribed RNA intermediate. Retrotransposons containing long terminal repeats have many of the attributes of retroviruses in animals but have not been previously observed to acquire a portion of a cellular gene as RNA tumor viruses do with oncogenes. We have found homology to plasma membrane proton ATPase genes within the Bs1 retrotransposon of maize, and this homology led us to clone the maize plasma membrane proton ATPase gene, which we have named Mha1. The sequence of Mha1 confirmed that 654 bp of this ATPase gene are present in Bs1; this segment represents the last amino acid of exon 4, all of exons 5 to 9, and part of exon 10. All introns have been removed from this acquired DNA, whereas 81 single base pair substitutions and a deletion of 183 bp in Bs1 differentiate these contiguous segments. The secondary mutations led to fewer changes in the derived Bs1 protein sequence than predicted for neutral events, suggesting that the acquired Mha1 DNA performs a selected function within Bs1. These data indicate that a retrotransposon can incorporate and transmit a portion of a standard nuclear gene transcript within its genetic material. Alternatively, these results suggest that Bs1 may represent a defective version of a plant retrovirus.

A maize cDNA clone was isolated by virtue of its intense hybridization to total maize genomic DNA, indicating homology to highly repetitive sequences. Genomic homologues were identified and subcloned from an adh1-bearing maize yeast artificial chromosome (YAC). Sequencing revealed that the expressed sequence was part of a Ty3-gypsy-type retrotransposon. We discovered and sequenced two complete retrotransposons of this family, and named them Cinful elements because they are members of a family of maize retrotransposons including Zeon-1 and the first plant transposable element sequenced, the solo long terminal repeat (LTR) called Cin1. All are defective, as Cinful-1 and Cinful-2 elements lack gag and Zeon-1 lacks pol homology. Despite the apparent lack of an intact "autonomous" element, the Cinful family has expanded to a copy number of about 18 000, representing just under 9% of the maize genome. Both point mutations and major rearrangements, including possible gene acquisition, differentiate members of the Cinful family. Cinful family members were found to have an unusual feature that we also observed in two other Ty3-class retrotransposons of teosinte and tobacco: related tandem repeats that separate their internal domains with a gag- or pol-containing homology from a 3' segment of unknown function. The conserved and variable features identified provide insights into the origin, mutational history, and functional components of this major constituent of the maize genome.

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