ax-Antitrypsin (AT), the major elastase inhibitor in mammalian serum, is produced primarily in the liver. We have characterized AT gene structure and expression in the mouse species Mus caroli, which expresses high levels of AT in the kidneys as well as in the liver. Analysis of cDNA and genomic clones showed that the AT gene in M. caroli exhibits high sequence homology (>90%) to the gene in laboratory mice (M. domesticus) throughout the coding and 5'-flanking regions. Despite this extensive sequence conservation, the functional organization of cis-acting regulatory elements governing liver-specific expression is strikingly different between these species. Transient-transfection assays showed that the proximal region of the M. caroli promoter (i.e., between -120 and -2 relative to the transcriptional start site) is 10-fold more active than the analogous region of M. domesticus in driving the expression of an indicator gene in cultured liver cells. The increased activity of the proximal region of the M. caroli AT promoter appears to be the result of one or both of the two base substitutions at positions -46 and -48. The weak proximal promoter in M. domesticus is compensated for by the presence of upstream, liver-specific enhancers between -199 and -520; the analogous region in M. caroli is inactive. Thus, during the course of evolution, the modest 7% sequence divergence that has occurred between the 5'-flanking regions of the AT genes in these two species has generated distinct, yet equally effective, modes of hepatocyte-specific expression.The molecular basis for the liver-specific expression of atl-antitrypsin (AT), a major seine protease inhibitor that functions in the control of neutrophil elastase activity (4, 29), has been intensely investigated in humans and mice. For the human gene, maximal liver-specific expression requires 261 nucleotides of the 5'-flanking region, which can be subdivided into a distal element located between -261 and -210 and two proximal elements located between -137 and -37 (6,8,26). Although the proximal elements function only in hepatic cells, the distal element acts as a nonspecific enhancer (8). In striking contrast, the mouse gene, which is structurally similar to the human gene, requires 500 bases of the upstream region for full activity (12); several domains that function specifically in hepatic cells and that interact with hepatocyte-enriched DNA binding proteins have been identified within this region (7, 12). Thus, liver-specific expression of the AT gene is maintained by different mechanisms in the two species, reflecting the accumulation of regulatory mutations since the two species diverged.With one known exception, all mammals express AT predominantly in the liver. The wild-derived mouse species Mus caroli, in sharp contrast to laboratory mice (M. domesticus), transcribes the AT gene in the kidneys as well as the liver (2,19,24). Renal AT expression in M. caroli is specific to tubule cells, where it is regulated by androgens during development (19). This species differe...