In rat liver, triiodothyronine (T3) and dietary carbohydrate induce the expression of the genes coding for malic enzyme (ME) (EC 1.1.1.40) and S14 protein. The mRNAs for both ME and S14 are elevated under circumstances associated with augmented lipogenesis. Since the lag time in the induction of mRNA coding for S14 is short (20 min) and the lag time in the induction of the mRNA for ME is relatively long (2-6 h), the possibility arose that the induction of the ME gene by T3 was mediated by S14 protein. To test this hypothesis we examined the temporal relationship between the accumulation of the hepatic S14 protein and the mRNAs coding for ME. In confirmation of previous reports, we found that two mRNAs coded for ME, one 27 S and the other 21 S in size. The level of enzyme activity generated appeared to be determined by both mRNA species. Sequencing of the 27 S fragment established that this mRNA is generated as a consequence of the use of an alternate polyadenylation site downstream to that used in the 21 S mRNA. Unanticipated from the earlier descriptions was the finding of a markedly asynchronous response of these mRNAs to T3 in hypothyroid animals. The lag time following T3 administration was 90 min for the 27 S and fully 8-12 h for the smaller 21 S sequence. Despite the rapid rise of mRNA S14, the S14 protein could not be detected for approximately 12 h after T3 administration. This ruled out the possibility that S14 is an obligate mediator in the induction of the ME gene. A contrasting pattern was observed in the euthyroid state where both ME mRNAs had indistinguishable lag times of 2-3 h, and the S14 protein rose within the same time frame. The delayed response of the 21 S mRNA for malic enzyme in hypothyroid animals thus appears to be due to a reversible defect in the transcription of the ME gene.