Genomic organization and structure of alpha-hydroxynitrile lyase in cassava (Manihot esculenta Crantz)

Two clones with homology to the alpha-hydroxynitrile lyase (HNL) cDNA clone, MeHNL10, were isolatedfrom a lambdaEMBL3 cassava (Manihot esculenta Crantz) genomic library. Analysis of the sequences showed that both genomic clones contain HNL genes (MeHNL4, MeHNL24) which are interrupted by two introns. RT-PCR analysis of MeHNL4 shows that it is expressed at high levels in seedling roots and at lower levels in cotyledons and young leaves. The deduced amino acid sequences of MeHNL4, MeHNL10, and MeHNL24 show high sequence identity and homology to the HNL from Hevea brasiliensis whose tertiary structure has been solved at 1.9-A resolution by X-ray crystallography. This high homology allowed the construction of model structures for all of the cassava proteins using the MODELLER program. Homology modeling indicates that the short variable exon 2 encodes the "cap" region which is thought to influence the substrate specificity of the protein. Two hybrid proteins were modeled using the core alpha/beta domain of MeHNL10 and the cap region of either the Hevea HNL or a structurally related Zea protein of unknown function. This analysis suggests that changes in the active site can be engineered by swapping exons.