Operon fusions for the Escherichia coli heat-labile enterotoxin type IIa (LT-IIa) operon were isolated and characterized. The LT-IIa genes are organized in a transcriptional unit similar to those of cholera toxin (CT) and the closely related E. coli heat-labile toxin type I (LT-I, with subtypes LTh-I and LTp-I). The nucleotide sequence of the LT-IIa genes was determined and compared with the sequences of LTh-I and CT. The A subunit gene of LT-IIa was found to be 57% homologous with the A subunit gene of LTh-I and 55% homologous with the A gene of CT. Most of the homology derived from the region of the A gene which encodes the Al fragment. The B gene of LT-IIa was not homologous with the B gene of LTh-I or CT. DNA probes containing various portions of the LT-Ila genes and adjacent sequences were used for hybridization studies with restriction endonuclease fragments of DNA from a collection of LT-II-producing strains. These studies showed that a probe containing much of the A subunit gene hybridized well to DNA from the various strains, but a probe for the B subunit gene did not.Escherichia coli heat-labile enterotoxin type I (LT-I, with subtypes LTh-I and LTp-I) and cholera toxin (CT) are structurally and antigenically related toxins capable of causing secretory diarrhea (11,12). Both toxins are composed of one A subunit which has an ADP-ribosylating activity and five B subunits which recognize and bind to ganglioside GM1 on eucaryotic cell surfaces (13,14,21,33,43). The A subunit of CT and LT-I undergoes a proteolytic cleavage that produces two fragments designated Al and A2, with the enzymatic activity residing in the Al fragment (15, 16). The genes for LT-I and CT have been sequenced, and comparisons of them show that they are related (8,25,29,44). The A subunit genes of CT and LTh-I are 78.6% homologous, and the B subunit genes are 78% homologous (45). We have recently described a second group of E. coli heat-labile enterotoxins, LT-II, which are not neutralized by antisera against CT and LT-I and cross-react very weakly with LT-I and CT, as determined by solid-phase radioimmunoassays (19,20). Two distinct members of the LT-II family, LT-IIa and LT-IIb, are now known, and both have A and B subunits which are similar in size to those of 20).LT-IIa possesses ADP-ribosylating activity for the G, subunit of adenylate cyclase similar to that of LT-I and CT (7). The ganglioside-binding specificities of the LT-IIa and LTIlb B subunits are different from each other and from those of CT and LT-I (S. Fukuta, J. L. Magnani, E. M. Twiddy, R. K. Holmes, and V. Ginsburg, manuscript submitted for publication).We cloned the genes for LT-IIa from the chromosome of E. coli strain SA53 and, through subcloning and minicell analysis, localized the A and B subunit genes (36). A DNA probe derived from both A and B gene sequences of LT-IIa failed to hybridize with LTp-I sequences (36). Since LT-IIa appears to be only distantly related to LT-I and CT from immunochemical and hybridization experiments, we wanted to examine further the ...