Serotonin N-acetyltransferase (AANAT) converts serotonin to N-acetylserotonin (NAS), a distinct biological regulator and the immediate precursor of melatonin, a circulating hormone that influences circadian processes, including sleep. N-terminal sequences of AANAT enzymes vary among vertebrates. Mechanisms that regulate the levels of AANAT are incompletely understood. Previous findings were consistent with the possibility that AANAT may be controlled through its degradation by the N-end rule pathway. By expressing the rat and human AANATs and their mutants not only in mammalian cells but also in the yeast Saccharomyces cerevisiae, and by taking advantage of yeast genetics, we show here that two "complementary" forms of rat AANAT are targeted for degradation by two "complementary" branches of the N-end rule pathway. Specifically, the N ␣ -terminally acetylated (Nt-acetylated) Ac-AANAT is destroyed through the recognition of its Nt-acetylated N-terminal Met residue by the Ac/N-end rule pathway, whereas the nonNt-acetylated AANAT is targeted by the Arg/N-end rule pathway, which recognizes the unacetylated N-terminal Met-Leu sequence of rat AANAT. We also show, by constructing lysineto-arginine mutants of rat AANAT, that its degradation is mediated by polyubiquitylation of its Lys residue(s). Human AANAT, whose N-terminal sequence differs from that of rodent AANATs, is longer-lived than its rat counterpart and appears to be refractory to degradation by the N-end rule pathway. Together, these and related results indicate both a major involvement of the N-end rule pathway in the control of rodent AANATs and substantial differences in the regulation of rodent and human AANATs that stem from differences in their N-terminal sequences.Arylalkylamine N-acetyltransferase (AANAT) 2 converts the neurotransmitter serotonin to N-acetylserotonin (NAS)(1-11). Regulatory functions of NAS include its activity as an agonist of TrkB, the receptor for the brain-derived neurotrophic factor (12)(13)(14). NAS is the immediate precursor of melatonin, a circulating hormone that regulates sleep and other circadian processes in vertebrates. Melatonin is also present in invertebrates, including insects, as well as in animals that lack recognizable neurons (1, 15-21). The functions of melatonin in mammals include the modulation of circadian rhythms in response to light-dark cycles. Melatonin also contributes to the control of seasonal physiology (20). These mechanisms are a part of a broader range of processes that involve distinct biological oscillators in all organisms (22-24). In the course of daily light-dark cycles, the activity of AANAT and the level of the ϳ23-kDa AANAT protein in the brain's pineal gland are high during nocturnal periods and rapidly decrease following exposure to light (1,20,25).In mammals, changes of AANAT levels in the brain's pineal gland are controlled by the circadian oscillator in the suprachiasmatic nucleus of the hypothalamus. At night, axons of rodent superior cervical ganglion neurons release norepinephrine i...