The mechanisms by which calmodulin coordinates its numerous molecular targets in living cells remain largely unknown. To further understand how this pivotal Ca2+-binding protein functions in vivo, we isolated and studied nine new Paramecium behavioral mutants defective in calmodulin. Nucleotide sequences of mutant calmodulin genes indicated single amino-acid substitutions in mutants cam4(E104K), cam5-l (D95G), cam6 (A102V), cam' (H135R), cam14-l (G59S) and cam15 (D50G). In addition, we encountered a second occurrence of three identified substitutions ; they are cam1-2 (SlOlF), c a d -2 (D95G) and cam14-2 (G59S). Most of these mutational changes occurred in sites that have been highly conserved throughout evolution. Furthermore, most of these changes were not among the amino acids known to interact with the basic amphiphilic peptides of calmodulin targets. Consistent with our previous finding [Kink, J. A., Maley, M. E., Preston R. R., Ling, K.-Y., C. (1990) Cell 62, 165-1741, mutants that under-reacted to certain stimuli (allele number above 10) had substitutions in the N-terminal lobe of calmodulin, and those that over-reacted (below 10) had substitutions in the C-terminal lobe. No mutations were found in the central helix that connects the lobes. Thus, through undirected in vivo mutation analyses of Paramecium, we discovered that each of the two lobes of calmodulin has a distinct role in regulating the function of a specific ion channel and eventually the behavior of Paramecium. We, therefore, propose a hypothesis of functional bipartition of calmodulin that reflects its structural bipartition.Ca2+ as a second messenger works through Ca2+-binding proteins. Among such proteins, calmodulin (CaM) stands out as being an activator of many enzymes as well as ion pumps and channels. The crystal structure of calmodulin has been resolved and refined [l -41. Ca2+ binding to the EF hands of calmodulin [5] and the disinhibition of target proteins through an interaction of the Ca2+-CaM complex with the basic amphiphilic a helix (BAA) of the target [6-101 have also been thorougly examined.The best known targets of calmodulin are some 20 different enzymes Ell]. Calmodulin also activates a Ca2+ pump in the erythrocyte membrane [12], which hydrolyses ATP and transports Ca" outward against the Ca" electrochemical gradient. There is evidence indicating that certain ion channels including photosensory ion channels of the Drosophila eye [13], ryanodine-receptor channel in the sarcoplasmic membranes [14], and the cyclic-nucleotide-activated channel of rat olfactory receptor neurons (Chen and Yau, unpublished results) are also regulated by Ca2+-CaM. Previous studies clearly show that Ca2+-CaM modulates several types of ion channels in Paramecium ; mutations that inhibit or reduce specific Ca2+-activated ion currents in vivo result from alterations in the single-copy calmodulin gene Despite the depth of our knowledge of calmodulin in vitro, its roles in vivo remain largely unclear. The wide target range and extreme evolutionary cons...