The complete set of genes encoding major intrinsic proteins in arabidopsisprovides a framework for a new nomenclature for major intrinsic proteins in plants

Major intrinsic proteins (MIPs) facilitate the passive transport of small p olar molecules across membranes. MlPs constitute a very old family of prote ins and different forms have been found in all kinds of living organisms, i ncluding bacteria, fungi, animals, and plants. In the genomic sequence of A rabidopsis, we have identified 35 different MIP-encoding genes. Based on se quence similarity, these 35 proteins are divided into four different subfam ilies: plasma membrane intrinsic proteins, tonoplast intrinsic proteins, NO D26-like intrinsic proteins also called NOD26-like MIPs, and the recently d iscovered small basic intrinsic proteins. In Arabidopsis, there are 13 plas ma membrane intrinsic proteins, 10 tonoplast intrinsic proteins, nine NOD26 -like intrinsic proteins, and three small basic intrinsic proteins. The gen e structure in general is conserved within each subfamily, although there i s a tendency to lose introns. Based on phylogenetic comparisons of maize (Z ea mays) and Arabidopsis MIPs (AtMIPs), it is argued that the general intro n patterns in the subfamilies were formed before the split of monocotyledon s and dicotyledons. Although the gene structure is unique for each subfamil y, there is a common pattern in how transmembrane helices are encoded on th e exons in three of the subfamilies. The nomenclature for plant MlPs varies widely between different species but also between subfamilies in the same species. Based on the phylogeny of all AtMIPs, a new and more consistent no menclature is proposed. The complete set of AtMIPs, together with the new n omenclature, will facilitate the isolation, classification, and labeling of plant MIPs from other species.