The Arabidopsis genome. An abundance of soluble N-ethylmaleimide-sensitive factor adaptor protein receptors

Abstract

Many factors have been characterized as essential for vesicle trafficking, including a number of proteins commonly referred to as soluble N-ethylmaleimide-sensitive factor adaptor protein receptor (SNARE) components. The Arabidopsis genome contains a remarkable number of SNAREs. In general, the vesicle fusion machinery appears highly conserved. However, whereas some classes of yeast and mammalian genes appear to be lacking in Arabidopsis, this small plant genome has gene families not found in other eukaryotes. Very little is known about the precise function of plant SNAREs. By contrast, the intracellular localization of and interactions between a large number of plant SNAREs have been determined, and these data are discussed in light of the phylogenetic analysis.

Figure 1

SNAREs in vesicle fusion. A, Syntaxins are usually found in an inactive state associated with a member of the Sec1p family. In some manner the Sec1 protein and other effectors activate the syntaxin, allowing it to associate with other SNAREs to form a t-SNARE complex. B, Four SNARE helicies are required for vesicle fusion to occur (labeled the a-, b-, c-, and d- helices as described in Scales et al., 2000). The a-helix is always contributed by a syntaxin residing on a target membrane. At certain targeting steps (e.g. at the PM) the syntaxin associates with a member of the SNAP25 class of SNAREs, which contributes a b- and c- helix to the t-SNARE complex (B, top right). Other steps, including at most intracellular membranes, the syntaxin associates with two other SNAREs who each contribute a b- or a c-helix to the t-SNARE complex (B, bottom right). C, Vesicle fusion likely occurs when the v-SNARE (or d-helix) from the vesicle assembles into a trans-SNARE complex (or SNAREpin) with the t-SNARE complex (here just showing the SNAP25-containing complex). For simplicity a single trans-SNARE complex is drawn; it is possible that the concerted action of many trans-SNARE complexes forming simultaneously may be required for a vesicle to fuse. D, The four-helix cis-SNARE complex results, where all four proteins are on the same membrane. The cis-SNARE complex is a binding site for SNAPs and NSF, proteins that disassociate the SNARE complex, freeing the individual SNAREs for future fusion events.

Figure 2

Arabidopsis syntaxin groups. The protein sequences of Arabidopsis syntaxins were aligned using default parameters of the CLUSTAL algorithm of the MEGALIGN program in the DNASTAR package. The resulting phylogenetic tree revealed the presence of eight groups (SYP1–8), which were numbered according to various criteria (see text). For those Arabidopsis syntaxins that have been previously published, the prior name is given in parenthesis. The accession numbers for all the Arabidopsis SNAREs can be acquired from http://www.msu.edu/∼sanderfo/atsnare.htm

Figure 3

Phylogenetic analysis of eukaryotic syntaxins. Full-length sequences of the Arabidopsis (At), yeast (Sc), and selected human (Hs) syntaxins were acquired from GenBank and aligned as described in Figure 2. Where it is known, the intracellular localization of the indicated syntaxins is given (see text for references). Because the nature of the endosomal compartments (i.e. early, late, prevacuolar, etc.) can vary considerably depending on the cell type we use the general term endosome (Endo) for those syntaxins localized to these types of endomembranes. Often, different researchers have found conflicting results with the same syntaxin and these are noted by an asterisk. More information on these sequences, as well as further alignments with other eukaryotic syntaxins, can be acquired from http://www.msu.edu/∼sanderfo/atsnare.htm.

Figure 4

Gene structure of the Arabidopsis syntaxins. The cDNA sequence of each Arabidopsis syntaxin is represented schematically as a line with the position of the introns indicated by the triangles. White triangles within each group indicate an identical intron position within a particular gene family and black triangles indicate introns in a position not found in other members of the gene family.

Figure 5

Phylogenetic analysis of Sec1 proteins from several eukaryotes. Protein sequences from representative Sec1p family members from yeast (Sc), Arabidopsis (At), Human (Hs), Rat (Rattus novernicus; Rn), fruit fly (Dm), and C. elegans (Ce) were acquired from GenBank and aligned as described in Figure 2. Where it is known the intracellular localization of Sec1 proteins is indicated. Note that although the closest homologs of AtSec1a, AtSec1b, and KEULE are the animal exocytic Sec1 proteins, the three Arabidopsis Sec1 proteins cluster as a somewhat separate group and may have evolved to play novel roles (such as cytokinesis in the case of KEULE).