Apolipoprotein (apo) B mRNA editing is the deamination of C 6666 to uridine, which changes the codon at position 2153 from a genomically encoded glutamine (CAA) to an in-frame stop codon (UAA). The apoB mRNA-editing enzyme complex recognizes the editing region of the apoB pre-mRNA with exquisite precision. Four sequence elements spanning 139 nucleotides (nt) on the apoB mRNA have been identified that specify this precision. In cooperation with the indispensable mooring sequence and spacer element, a 5 efficiency element and a 3 efficiency element enhance editing in vitro. A phylogenetic comparison of 32 species showed minor differences in the apoB mRNA sequence, and the apoB mRNA from 31 species was robustly edited in vitro. However, guinea pig mRNA was poorly edited. Compared with the consensus sequences of these 31 species, guinea pig apoB mRNA has three variations in the 3 efficiency element, and the conversion of these to the consensus sequence increased editing to the levels in the other species. From this information, a model for the secondary structure was formulated in which the mooring sequence and the 3 efficiency element form a doublestranded stem. Thirty-one mammalian apoB mRNA sequences are predicted to form this stem positioning C 6666 two nucleotides upstream of the stem. However, the guinea pig apoB mRNA has a mutation in the 3 efficiency element (C 6743 to U) that predicts an extension of the stem and hence the lower editing efficiency. A test of this model demonstrated that a single substitution at 6743 (U to C) in the guinea pig apoB mRNA, that should reduce the stem, enhanced editing, and mutations in the 3 efficiency element that extended the stem for three base pairs dramatically reduced editing. Furthermore, the addition of a 20-nucleotide 3 efficiency element RNA, to a 58-nucleotide guinea pig apoB mRNA lacking the 3 efficiency element more than doubled the in vitro editing activity. Based on these results, a model is proposed in which the mooring sequence and the 3 efficiency element form a double-stranded stem, thus suggesting a mechanism of how the 3 efficiency element enhances editing.RNA editing is the alteration of the genetic information present in nascent RNA transcripts. One form of RNA editing, apolipoprotein (apo) 1 B mRNA editing, is the deamination of a specific cytidine (C 6666 ) by an editing complex consisting of the editing enzyme APOBEC-1 (apoB mRNA editing enzyme catalytic polypeptide 1) and one or more as yet unidentified auxiliary proteins (1-7). The resulting U changes codon 2153 from a genomically encoded CAA (glutamine) to an in-frame stop codon (UAA) (8, 9). ApoB mRNA editing, which occurs in the intestine of all mammals, results in the formation of a truncated apoB protein (apoB-48) that is 48% of the size of the full-length genomically encoded apoB (apoB-100) (10, 11).The apoB mRNA editing occurs with exquisite precision. The apoB mRNA editing complex locates the apoB pre-mRNA among tens of thousands pre-mRNAs (12,13). No other mRNAs have been identified that ...