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The complete set of genes encoding major intrinsic proteins in Arabidopsis provides a framework for a new nomenclature for major intrinsic proteins in plants - PubMed

Comparative Study

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

U Johanson et al. Plant Physiol. 2001 Aug.

Abstract

Major intrinsic proteins (MIPs) facilitate the passive transport of small polar molecules across membranes. MIPs constitute a very old family of proteins and different forms have been found in all kinds of living organisms, including bacteria, fungi, animals, and plants. In the genomic sequence of Arabidopsis, we have identified 35 different MIP-encoding genes. Based on sequence similarity, these 35 proteins are divided into four different subfamilies: plasma membrane intrinsic proteins, tonoplast intrinsic proteins, NOD26-like intrinsic proteins also called NOD26-like MIPs, and the recently discovered small basic intrinsic proteins. In Arabidopsis, there are 13 plasma membrane intrinsic proteins, 10 tonoplast intrinsic proteins, nine NOD26-like intrinsic proteins, and three small basic intrinsic proteins. The gene structure in general is conserved within each subfamily, although there is a tendency to lose introns. Based on phylogenetic comparisons of maize (Zea mays) and Arabidopsis MIPs (AtMIPs), it is argued that the general intron patterns in the subfamilies were formed before the split of monocotyledons and dicotyledons. Although the gene structure is unique for each subfamily, there is a common pattern in how transmembrane helices are encoded on the exons in three of the subfamilies. The nomenclature for plant MIPs 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 nomenclature is proposed. The complete set of AtMIPs, together with the new nomenclature, will facilitate the isolation, classification, and labeling of plant MIPs from other species.

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Figures

Figure 1
Figure 1

Phylogenetic comparison of the complete set of 35 different MIPs encoded in the Arabidopsis genome. Plant MIPs are divided into four distinct subfamilies: PIPs, TIPs, NIPs, and SIPs. Similar proteins within a subfamily, with a maximum of 30% divergence, are clustered in monophyletic groups. The first and the last digit in the protein name identify the group and the individual gene product, respectively. This tree was obtained using the whole alignment and the distance method. Omitting the none-conserved N- and C-terminal regions from the phylogenetic analysis does not break the defined groups; only the relative positions of PIP2;6 and TIP3s is changed. In this case PIP2;6 forms a separate branch between PIP2;4 and PIP2;5 and TIP3s branch between TIP2s andTIP4;1. The bar indicates the mean distance of 0.05 changes per amino acid residue.

Figure 2
Figure 2

Bootstrap majority-rule consensus tree generated with the distance method. A bootstrap value of 100% indicates branches that were supported in all replicates of resampling of data. Branches with a bootstrap value of less than 50% are collapsed.

Figure 3
Figure 3

Schematic structure of MIP encoding genes in Arabidopsis. Horizontal bars and gaps depict exons and intron positions, respectively. Parts encoding transmembrane helices H1 to H6 according to an alignment with GlpF are indicated by vertical bars. The color on the vertical bars shows homologous transmembrane helices in the first and second halves of the MIPs. The exons and transmembrane helices are drawn to scale but the positions of helices are schematic. Helices encoded on two exons are only indicated on the exon where the major part is encoded. Small indels in the alignment of different genes, positioned between two helices on the same exon, are not shown.

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