Download Increases in the Number of SNARE Genes

Genome Analysis
Increases in the Number of SNARE Genes Parallels the
Rise of Multicellularity among the Green Plants1[W][OA]
Anton Sanderfoot*
Department of Plant Biology, University of Minnesota, St. Paul, Minnesota 55108
The green plant lineage is the second major multicellular expansion among the eukaryotes, arising from unicellular ancestors
to produce the incredible diversity of morphologies and habitats observed today. In the unicellular ancestors, secretion of
material through the endomembrane system was the major mechanism for interacting and shaping the external environment.
In a multicellular organism, the external environment can be made of other cells, some of which may have vastly different
developmental fates, or be part of different tissues or organs. In this context, a given cell must find ways to organize its
secretory pathway at a level beyond that of the unicellular ancestor. Recently, sequence information from many green plants
have become available, allowing an examination of the genomes for the machinery involved in the secretory pathway. In this
work, the SNARE proteins of several green plants have been identified. While little increase in gene number was seen in the
SNAREs of the early secretory system, many new SNARE genes and gene families have appeared in the multicellular green
plants with respect to the unicellular plants, suggesting that this increase in the number of SNARE genes may have some
relation to the rise of multicellularity in green plants.
The flowering plants are the most recent of a long
lineage of green plants that first set to land nearly 450
million years ago in the Ordovician period (for review,
see Sanderson et al., 2004). In turn, the early land
plants arose from a group of aquatic green algae
related to Chara, which themselves are related to
familiar unicellular green algae like Chlamydomonas.
Thus, the multicellular plants arose from unicellular
ancestors completely independent from the animal
lineage, and represent a chance to examine a distinct
way to assemble a multicellular organism. Multicellularity requires both the ability to perform as a cell and
as part of a larger entity. One major requirement for
both of these abilities is the proper management of the
endomembrane system, since within a multicellular
organism, the neighbors of a given cell can have a different developmental fate, be part of a different tissue,
or even a different organ. Basically, different neighbors
may require different aspects of cell-to-cell signaling
(developmental signals, cell wall components, etc.),
and thus it becomes important to control the secretory
aspects of the cell. Thanks to the large-scale sequencing and annotation of many green plant genomes, we
1
This work was supported by the Department of Plant Biology at
the University of Minnesota, Twin Cities, and by a Grant-in-Aid
award from the graduate school of the University of Minnesota.
* E-mail [email protected]; fax 612–625–1738.
The author responsible for distribution of materials integral to the
findings presented in this article in accordance with the policy
described in the Instructions for Authors (www.plantphysiol.org) is:
Anton Sanderfoot ([email protected]).
[W]
The online version of this article contains Web-only data.
[OA]
Open Access articles can be viewed online without a subscription.
www.plantphysiol.org/cgi/doi/10.1104/pp.106.092973
6
can now examine some of the molecular basis of how
one major player in the endomembrane system has
evolved during the rise of multicellular plants, that of
the SNARE family of proteins.
Proteins of the SNARE family function as molecular
machines, self-assembling into a cluster of four coiledcoil helices that drive membrane fusion (for review, see
Hong, 2005). The helices, termed Qa, Qb, Qc, and R are
each contributed by individual SNARE proteins, except
in the SNAP25 family, which carries two SNARE helices
(Qb and Qc) in a single protein. As a vesicle forms at
the donor membrane, a single type of SNARE is incorporated into the vesicle membrane. Termed a vesicle
(v)-SNARE, this protein has some level of specificity in
its ability to interact with a cognate set of target
(t)-SNAREs that contribute the other helices. The classic
example is the mammal synaptic complex where the
v-SNARE of the synaptic vesicle, R-synaptobrevin/
VAMP-2, interacts with the presynaptic t-SNARE complex of Qa-Syntaxin and Qb 1 Qc-SNAP25 (Hong,
2005). Similarly, the v-SNARE of the endoplasmic
reticulum (ER)-derived COPII vesicle, Qc-Bet1p, interacts with the cis-Golgi t-SNARE complex of Qa-Sed5p,
Qb-Bos1p, and R-Sec22p (Hong, 2005). This theory has
been well supported by both in vivo and in vitro
systems, and likely represents the typical situation
throughout the endomembrane system of eukaryotes.
Full genome sequence assemblies have been produced for three angiosperms, two dicots and one
monocot: Arabidopsis (Arabidopsis thaliana; eudicot:
eurosids: malvids: Brassicales), Populus trichocarpa
(eudicot: eurosid: fabids: Malpighiales), and rice (Oryza
sativa; monocot: commelinids: Poales). In addition, four
chlorophyte algae have also been sequenced: Chlamydomonas reinhardtii (Chlorophyta: Chlorophyceae), Volvox carteri (Chlorophyta: Chlorophyceae), Ostreococcus
Plant Physiology, May 2007, Vol. 144, pp. 6–17, www.plantphysiol.org Ó 2007 American Society of Plant Biologists
Downloaded from on June 16, 2017 - Published by www.plantphysiol.org
Copyright © 2007 American Society of Plant Biologists. All rights reserved.
The SNARE Proteins of Green Plants
tauri, and Ostreococcus lucimarinus (Chlorophyta: Prasinophyceae). Recently, these extremes of the green plant
lineage were connected with the release of the genome
sequence of the moss Physcomitrella patens (Bryophyta).
For each of these genome sequences, all genes of the
SNARE family were identified and classified with
respect to the major clades identified in previous analyses of the Arabidopsis SNAREs (Sanderfoot et al.,
2000; Pratelli et al., 2004; Uemura et al., 2004), the rice
SNAREs (Sutter et al., 2006), and a recent algorithmbased analysis of SNAREs for several sequenced eukaryotes (Yoshizawa et al., 2006). In addition to those
clades, some additional SNAREs were identified from
new information in other organisms, and by comparison among the green plant sequences.
Overall, the number of SNARE-encoding genes increases among the land plants compared to the unicellular plants. In addition to an increase in the net
number of genes, new gene families and subfamilies
appear among the SNARE genes with products that are
associated with secretion and with the endosomal system. The increase in gene number for the endosomal
SNAREs might be associated with the development of
the typical large central vacuole morphology of the
plant cell. Meanwhile, the large increase in genes
encoding secretory SNAREs seems to occur in multicellular plants in comparison to their presumed unicellular ancestors. Others have hypothesized that these
kinds of increases in gene number may be associated with the rise of multicellularity (e.g. Dacks and
Doolittle, 2002). For example, once the cell above is
different from the cell beside, it may become important
to be able to deliver different material (cell-cell signals,
extracellular matrix components, etc.) to the top of the
cell than to the side. One mechanism for this polarization of secretion can be provided by duplication and
specialization of the secretory SNAREs. Already, some
evidence support the specialization of secretory SNAREs
in distinct processes (Lukowitz et al., 1996; Collins
et al., 2003; Sutter et al., 2006). Collecting and identifying the potentially specialized SNAREs of the green
plants with particular achievements in multicellularity
may lead to more efficient studies of this process.
RESULTS AND DISCUSSION
Examining the sequences available from many eukaryotes has indicated that most eukaryotes have a
common set of SNARE proteins, a core set that likely
represents the genes from the last common ancestor of
the extant eukaryotes (Table I; Dacks and Doolittle,
2002, 2004; Yoshizawa et al., 2006). Often, SNAREs that
are single genes in unicellular organisms are present as
small gene families, or even seem to have diverged
into novel gene families that have gained specialized
functions in several organisms. In particular, an increase in the net number of SNARE-encoding genes is
seen in at least two places, among the green plants and
among the animals (Fig. 1). This observation that the
increase in SNAREs may be associated with the rise of
multicellularity in animals and land plants has been
made before (Dacks and Doolittle, 2002), though the
increase in the sequence information from the presumed unicellular ancestors of these groups has produced more support for this hypothesis.
Overall, the green plants examined in this work
have a remarkably consistent and homologous set of
SNARE proteins that generally recapitulate their presumed evolutionary relationships (see below). In contrast, based upon the genome sequences of two
unicellular thermoacidophilic red algae and EST evidence from the multicellular red algae Porphyra yezoensis, the SNARE proteins of the red algae are no
more similar to those of the green plants than either
are to the heterokont diatoms or oomycetes (see below
for examples). Therefore, even though red algae are
often considered to be a part of a larger plant kingdom
along with the green and glaucophyte algae (defined
by those organisms that are descendants of the primary plastid symbiosis; see Cavalier-Smith, 1998; Adl
et al., 2005), this work will focus on the more clearly
monophyletic green lineage (i.e. green plants).
The SNAREs of the Early Secretory Pathway Have
Changed Little in Land Plants
Green plants have proteins similar to the yeast
(Saccharomyces cerevisiae) or mammalian SNAREs that
operate between the ER and Golgi apparatus (Fig. 2;
Supplemental Figs. S1, S2, and S6; Table I). In yeast
cells, the SNARE complex that mediates retrograde
traffic back to the ER seems to consist of Qa-Ufe1p 1
Qb-Sec20 1 Qc-Use1p 1 R-Sec22p (for review, see
Hong, 2005). As in mammals, plants have proteins that
are similar to each of these SNAREs: Qa-SYP81, QbSEC20, Qc-USE1, and R-SEC22. These proteins are
found in all angiosperms examined, and also in the
chlorophyte algae, indicating that this complex was
inherited vertically through the green plant lineage. In
some angiosperms, multiple copies of some of these
genes have been identified in completely sequenced
genomes, though any specialized functions for the
additional copies have not been examined. Due to a
misannotation in an early version of the Arabidopsis
genome, the gene encoding Qc-USE11 (At1g54110)
was fused to an adjacent gene that encodes a cation
exchanger (CAX10; At1g54115). Though this gene
model was later split, the CAX10 name stayed with
the USE1-encoding gene, and has subsequently been
passed through annotation of several other plant genomes (and missed in the Yoshizawa et al., 2006
analysis). Nonetheless, this gene does encode a protein
with a structure similar to other SNARE proteins,
groups with the USE1-like genes of animals and fungi
in phylogenetic analysis (Supplemental Fig. S1) and is
found in all green plants (Table I).
Similarly, proteins similar to those of the yeast or
animal Golgi SNARE complex (Hong, 2005) are also
found in green plants: Qa-SYP3, Qb-MEMB1, Qc-BET1,
Plant Physiol. Vol. 144, 2007
7
Downloaded from on June 16, 2017 - Published by www.plantphysiol.org
Copyright © 2007 American Society of Plant Biologists. All rights reserved.
Sanderfoot
Table I. Major groups of green plant SNAREs (with outgroups)
As, Angiosperms; Gs, gymnosperms; Bp, bryophytes (mosses); Ch, Chlorophyceae; Pr, Prasinophyceae; Rp, rhodophytes; Hk, heterokonts; Am,
amoebozoa; Fn, fungi; An, animals; *, at least one SNARE of this type is present. When one has been assigned, a KOG number is given. Group names
in bold represent green-plant-specific groups or subgroups.
Green Plants
Qa-SNAREs
Qa-SYP8
Qa-SYP3
Qa-SYP4
Qa-SYP2
Qa-SYP1
SYP13
SYP12
SYP11/KNOLLE
PEN1/ROR2
SYP124
Qb 1 Qc-SNAREs
SNAP33
Qb-SNAREs
Qb-SEC20
Qb-MEMB1
Qb-GOS1
Qb-VTI1
Qb-NPSN1
Qc-SNAREs
Qc-USE1
Qc-BET1
plant-SFT1
Qc-SYP6
Qc-SYP5
Qb-SYP7
R-SNAREs
R-SEC22
R-YKT6
R-VAMP71
VAMP711
VAMP714
R-VAMP72
VAMP721
VAMP727
VAMP724
R-brevins
R-tomosyn
As
Gs
Bp
Ch
Pr
Rp
Hk
Am
Fn
An
KOG3894
KOG0812
KOG0809
KOG0811
KOG0810
–
–
–
–
–
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
KOG3065
*
*
*
*
*
*
*
–
KOG3251
KOG3208
KOG1666
–
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
–
KOG3385
–
KOG3202
–
–
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
KOG0862
KOG0861
KOG0859
–
–
KOG0859
–
–
–
KOG0860
KOG1983
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
and R-SEC22. Investigations into a few of these genes
has indicated that the Arabidopsis proteins function
similar to the yeast and animal homologs (Chatre et al.,
2005). Again, these proteins are present in all green
plants (Fig. 2; Supplemental Figs. S2, S3, S5, and S6).
In Arabidopsis, two of these genes (SYP31 and SYP32)
may have specialized functions: Instead of the cis-Golgi,
SYP31 is found on the peripheral ER and may participate in a specialized role in cytokinesis (Rancour
et al., 2002).
Later in the Golgi stacks, it has been shown that
some of the SNAREs in the early Golgi complex are
replaced by other SNAREs (Parlati et al., 2002; Volchuk
et al., 2004). In mammals, Qb-Membrin is replaced by
Qb-GS28 and Qc-mBet1 is replaced by a related pro-
*
tein (Qc-GS15; Volchuk et al., 2004). Plants also have
homologs of the Qb-GS28/Gos1p and a BET1-like
protein called Qc-SFT1 (Table I; Fig. 2; Supplemental
Figs. S2, S3, and S5). An annotation error led to the
association of the Arabidopsis SFT1-family genes with
the KOG (clusters of orthologous groups for eukaryotic complete genomes; Tatusov et al., 2003) for the
mitochondrial termination factor (KOG1267). This led
to spread of this name for the SFT1-like genes throughout subsequent autoannotations of genomes. As with
USE1, the plant SFT1-like genes have a clear SNARElike structure and group within the brevin-like QcSNAREs (Supplemental Fig. S5), suggesting that it is
reasonable to identify these as a green plant-specific
clade of SNARE.
8
Plant Physiol. Vol. 144, 2007
Downloaded from on June 16, 2017 - Published by www.plantphysiol.org
Copyright © 2007 American Society of Plant Biologists. All rights reserved.
The SNARE Proteins of Green Plants
Figure 1. SNARE genes in several eukaryotic genomes. SNAREs are divided into three basic modules based upon the site of
action: ER/Golgi, TGN/endosomal (including vacuole), and secretory/PM. Among the unicellular eukaryotes, this division is
based upon homology to SNAREs with known functions and does not exclude multiple roles for some proteins (especially in
Cyanidioschyzon where the Qb, Qc, and R roles in secretion must be played by proteins from other modules). SNARE genes are
indicated by individual boxes with the type of SNARE labeled with a color (Qa, orange; Qb, purple; Qb 1 Qc, violet; Qc, red; R,
blue). Each box indicates a single genomic locus and does not include alternatively spliced isoforms of SNARE genes that are
common in some lineages (especially vertebrates). Lineages are specified to the left with arrows indicating relationships among
the major groups (Adl et al., 2005): Green, Green plants; embryo., embryophytes (land plants); chloro., chlorophytes (green
algae); red, red algae; hetero., heterokonts (brown algae, diatoms, oomycetes); amoeba, amoebozoa (slime molds); fungi;
animals. Species abbreviations: Arath, Arabidopsis; Poptr, P. trichocarpa; Orysa, O. sativa; Phypa, P. patens; Chlre, C.
reinhardtii; Volca, V. carteri; Ostta, O. tauri; Ostlu, O. lucimarinus; Cyame, Cyanidioschyzon merolae; Thaps, Thalassiosira
pseudonana; Phatr, Phaeodactylum tricornutum; Physo, Phytophthora sojae; Phyra, Phytophthora ramorum; Dicdi, Dictyostelium discoideum; Sacce, S. cerevisiae; Schpo, Schizosaccharomyces pombe; Caeel, Caenorhabditis elegans; Drome,
Drosophila melanogaster; Homsa, Homo sapiens.
Additional Endosomal SNARE Genes May Be Associated
with Development of the Large Central Vacuole
At the far end of the Golgi complex are those
complexes of the trans-Golgi network (TGN) that function in anterograde traffic from earlier Golgi stacks or
in retrograde traffic from the endosomes. Plants again
have the SNAREs similar to the mammal and fungal
proteins that are posited to be involved in these steps
(Fig. 2; Supplemental Figs. S2–S4, and S6). In green
plants, Qa-SYP4 is similar to mammalian syntaxin 16
or fungal Tlg2p, and at least in Arabidopsis, has been
shown to localize to the TGN like the mammalian
equivalents (Bassham et al., 2000). Some plants have
multiple copies of Qa-SYP4, and in Arabidopsis, SYP41
and SYP42 have been shown to localize to distinct
domains of the same TGN (Bassham et al., 2000), indicating some functional distinction. Qa-SYP41 has
been shown to interact with Qb-VTI12 and Qc-SYP61
(Bassham et al., 2000), similar to homologous proteins
from yeast and mammals (Mallard et al., 2002), and to
also interact with R-YKT6 in Arabidopsis (Chen et al.,
2005). It was also shown that Qa-SYP41 can distinguish
between two members of the Qb-VTI1 gene family, indicating that some specialization has occurred among
the multiple copies of these SNAREs in angiosperms
(Bassham et al., 2000; Sanderfoot et al., 2001).
Defining the SNARE complexes that function in the
late endosomes and vacuole/lysosomes has been difficult and may be very lineage specific. For example,
yeast has two Qa-SNAREs that are functionally distinct: Pep12p that functions on the late endosome/
prevacuolar compartment and Vam3p that functions
on the vacuole (for review, see Burri and Lithgow,
2004). Meanwhile, most other fungi have only a single
Pep12p-like Qa-SNARE. Mammals also have two related Qa-SNAREs, syntaxin 7 and syntaxin 13, that
may also have a functional distinction between the
lysosome and endosomes (Mullock et al., 2000; Sun
et al., 2003); though, again, some animals have only
one Qa-SNARE that presumably does both. Similarly,
while chlorophyte algae have a single Qa-SYP2, angiosperms often have multiple genes that appear to
have functional differences. For example, in Arabidopsis, SYP21 appears to function on the late endosomes, while SGR3/SYP22 functions on the vacuole
(Rojo et al., 2003; Yano et al., 2003). Regardless, these
Qa-SNAREs each make complexes with Qb-VTI11 and
Qc-SYP5 (homologous to mammalian syntaxin 8; Supplemental Fig. S4), and like Qa-SYP41, can distinguish
between Qb-VTI11 and -VTI12 (Sanderfoot et al., 2001).
The R-SNARE partner has yet to be conclusively
demonstrated, but preliminary indications are that
R-YKT61 can interact with each of these SNARE complexes (A. Sanderfoot, unpublished data). Moreover,
members of the R-VAMP71 clade have been shown to
localize to the vacuolar membrane (Carter et al., 2004;
Uemura et al., 2004), suggesting that these may also be
involved with vacuolar/late endosomal trafficking
Plant Physiol. Vol. 144, 2007
9
Downloaded from on June 16, 2017 - Published by www.plantphysiol.org
Copyright © 2007 American Society of Plant Biologists. All rights reserved.
Sanderfoot
Figure 2. Clustering of SNARE gene families among eukaryotic groups. SNARE-encoding genes from several fully sequenced
eukaryotes are indicated by boxes as described in Figure 1. Hatched boxes in the row for pine (Pinta, Pinus taeda) indicate that
these genes are derived from searches of the EST database only and likely represent an underestimate of the number of SNARE
genes in this organism. Each vertical stack of boxes indicates a particular related group of SNARE proteins (see Supplemental
Figs. S1–S6) with the names given to the plant groups across the top and to the vertebrate groups across the bottom. See Figure
1 for abbreviations and notations. See Supplemental Table S1 for a list of individual genes for each organism.
similar to the some of the roles indicated for VAMP7 in
mammals (Ward et al., 2000; Pryor et al., 2004). This
role may have been elaborated in the land plants
because a second clade of VAMP71-type SNAREs (the
VAMP714-like subgroup) was found in angiosperms
(Table I; Fig. 2), though in the absence of experimental
evidence, the role of this angiosperm-specific subclade
is unclear. Ultimately, this very complicated and essential (Rojo et al., 2001) region of the plant cell will
require further study to clearly identify the roles for
the different complexes in traffic to and from the endosomes and the vacuole.
Is the Expansion of Secretory SNAREs Associated
with Multicellularity?
The land plants have greatly expanded the more
simple complement of secretory SNAREs present in
their unicellular ancestors (Fig. 1; Supplemental Figs. S1
and S6). Among green plants, it is likely that SYP1
(and related proteins) represents the Qa-SNAREs of
the plasma membrane (PM), which work along with
a Qb 1 Qc-SNARE similar to Arabidopsis SNAP33 (or
alternately with the Qb-NPSN1 and Qc-SYP7). Lacking brevins, green plants are widely believed to use a
special branch of the VAMP7-type R-SNAREs, the
VAMP72-clade, which appears to be specific to green
plants (Table I; Supplemental Fig. S6). Many members
of the VAMP72-type of SNARE have been localized to
the PM in Arabidopsis (Uemura et al., 2004), though
that these proteins act as the R-SNARE for a secretory
complex has yet to be shown conclusively. Since both
the Qa-SYP1 and the VAMP7 clades have greatly increased among the transition from chlorophytes to land
plants (Fig. 2), these groups deserve more investigation.
The SYP1 Lineage and Specialization and Differentiation
Among the vertebrates, many distinct types of QaSNAREs (syntaxins) reside on the PM (syntaxins 1, 2,
3, 4, 11, and 19) that have diverse and specialized
functions in delivery of vesicles to various domains of
the PM (Hong, 2005). Other animals typically have a
syntaxin 1-like protein and then at least one other
SNARE distantly related to this syntaxin 1 to 4 clade
(Bock et al., 2001). Fungi tend to have a single (or a
paralogous pair) of PM-type syntaxins (e.g. Burri and
Lithgow, 2004), as do most other unicellular eukaryotes that have been examined (Fig. 3). Others have
argued that this diversity of vertebrate syntaxins reflects their complex multicellular lifestyle in contrast
to their simpler unicellular ancestors (Bock et al., 2001;
Dacks and Doolittle, 2002).
Based on phylogenetic analysis, the single-copy chlorophyte SYP1 lies at the base of the embryophyte SYP1
clade (Fig. 3). Among the embryophytes, the SYP1 clade
splits into two large, well-supported groups: SYP12 and
SYP13 (Fig. 3). A common feature of the genes of the
SYP13 group is that all have multiple introns, almost all
of which occur at equivalent positions with the open
10
Plant Physiol. Vol. 144, 2007
Downloaded from on June 16, 2017 - Published by www.plantphysiol.org
Copyright © 2007 American Society of Plant Biologists. All rights reserved.
The SNARE Proteins of Green Plants
Figure 3. Qa-SNAREs of the PM have greatly
expanded in the land plants. Full-length protein
sequences of the Qa-PM orthologs from various
organisms were aligned by ClustalW, distances
were estimated with a neighbor-joining algorithm
and visualized in a phylogram. The tree was
rooted using the Qa-PM SNAREs of heterokonts.
Bootstrap support is indicated to the left of
branches. The clades and subclades of land plant
syntaxins are also indicated as described in the
text (also see Supplemental Fig. S7). See Figure
1 for species abbreviations.
reading frames (Supplemental Fig. S7). Little work has
been done on this type of syntaxin in the land plants,
aside from the finding that the protein is found on the
PM when overexpressed in Arabidopsis protoplasts
(Uemura et al., 2004) and that it plays some role in
Rhizobium symbiogenesis in legumes (Catalano et al.,
2007). The second group of PM syntaxins, the SYP12
group, includes members from all the embryophytes
examined (Fig. 3). The SYP12 group is distinct from the
SYP13 in that all the genes are encoded by a single exon,
or have only one intron, typically in an equivalent
position within the ORF (Supplemental Fig. S7). Like
the SYP13 group, members of the SYP12 group have
been shown to be found on the PM and be involved in
aspects of secretion (Lauber et al., 1997; Geelen et al.,
2002). The SYP12 group is itself split into three reasonably well-supported subgroups (Fig. 3).
A preangiosperm subgroup includes all of the
SYP12-like proteins from moss and SYP12-like proteins found encoded in the EST collections of gymnosperms (Fig. 3). The angiosperm SYP12 subgroup is
represented in two further subgroups, the PEN1/
ROR2 and the SYP124-like subgroups. In addition to
a role in general secretion (Geelen et al., 2002), the
PEN1/ROR2 subgroup may have taken on a specialized role in defense to fungal pathogens (Collins et al.,
2003; Nühse et al., 2003; Assaad et al., 2004). Arabidopsis mutants that lack both members of the PEN1/
ROR2 subgroup (i.e. syp121/pen1, syp122 double mutants) are severely dwarfed and show necrosis (Assaad
et al., 2004), suggesting that the function of the subgroup cannot be completely replaced by the SYP124
subgroup. Nonetheless, any specialized role for the
SYP124 subgroup syntaxins among the angiosperms
has yet to be shown. The third subgroup of SYP12
syntaxins is represented by the SYP11 group. A SYP11like protein is encoded among the gymnosperm ESTs
(Fig. 3), suggesting that this group may be common to
all the seed plants, though no SYP11-like protein is
found in the moss genome. Among the angiosperms,
this class of syntaxin is best represented by the
KNOLLE-like proteins. In Arabidopsis, KNOLLE protein is produced only during cell division, is found on
the cell plate, and is essential for completion of cytokinesis (Lukowitz et al., 1996; Lauber et al., 1997).
Interestingly, the cell-plate-mediated form of cytokinesis is found throughout all the land plants and is
even found in many green algae (Lopez-Bautista et al.,
Plant Physiol. Vol. 144, 2007
11
Downloaded from on June 16, 2017 - Published by www.plantphysiol.org
Copyright © 2007 American Society of Plant Biologists. All rights reserved.
Sanderfoot
2003), suggesting that other PM syntaxins must mediate this process in plants that lack the SYP11 group,
and that KNOLLE was a later invention of the seed
plants. A further subgroup of PM syntaxins (SYP112)
is found only among the eudicots Arabidopsis and
poplar (Fig. 3), and no obvious relative to SYP112 has
been found in the EST databases of other eudicots.
Because this clade is only found in two complete
genomes and has no known role (Muller et al., 2003), it
is unclear what role this SNARE may play.
The presence of three major groups (and several
subgroups) of PM syntaxins suggests a complexity and
specialization of roles that occurs at a point in evolutionary time coincident with the rise of land plants and
the associated multicellularity (see Fig. 5). The hypothesis that the expansion of the plant PM syntaxins may
be linked to multicellularity has been made before (e.g.
Dacks and Doolittle, 2002), but the new information in
this work now suggests this point clearly lies closer to
the radiation of the land plants. One could hypothesize
that the SYP13 group represents the basal PM syntaxin
inherited vertically from the chlorophyte ancestors,
and would be involved in general housekeeping roles
(e.g. constitutive secretion). The SYP12 group would
arise in the mosses (or earlier) to support more specialized roles of secretion (e.g. defense related, or
perhaps cell-plate formation). Finally, a specialized
syntaxin (SYP11/KNOLLE) would evolve to exclusively operate the essential process of cytokinesis in the
seed plants (or earlier). Later specializations (PEN1/
ROR2 and SYP124) would arise to further differentiate
some additional functions. Intensive research into
members of these clades in particular model systems
may support this hypothesis, as could additional sequence information from other plants that lie at evolutionarily significant points.
The VAMP7 Lineage in the Green Plants
Within the animal and fungi lineage, the brevins
serve the functions associated with secretion (Hong,
2005), and some other lineages (e.g. Dictyostelium) have
similar brevins that may act similarly (Supplemental
Table S1). On the other hand, the only potential brevins
in the green plant lineage are found in Chlamydomonas,
where a paralogous pair of genes (VAMP like or
VMPL) with unknown function are found. Instead,
plants only have the longin types of R-SNARE (Fig. 2;
Supplemental Fig. S6). Longin proteins have a conserved N-terminal domain that contains a profilinrelated fold that is also found in other non-SNARE
proteins (Rossi et al., 2004). In particular, plants have a
large group of longin SNAREs similar to the mammalian VAMP7 (Table I). In mammals, VAMP7 (also called
TI-VAMP) is involved in intraendosomal trafficking as
well as specialized aspects of exocytosis (Pryor et al.,
2004). Green plants seem to have two major groups of
VAMP7-like proteins (Table I; Supplemental Fig. S6).
The VAMP71 group is most similar to the mammalian
VAMP7 and likely plays a similar role to the mammalian VAMP7 in the endosomal system (see above). On
the other hand, the second group (VAMP72) appears to
be specific to the green plant lineage (Table I; Fig. 4)
and likely represents the R-SNARE component for
secretion among the green plants.
As in the VAMP71 group (see above), there has been
a divergence among the VAMP72 group in the seed
plants, where VAMP724 and VAMP727 subgroups can
be identified (Table I; Fig. 4). Some results have indicated that the VAMP727 of Arabidopsis is localized to
the early endosomes while other VAMP72 gene family
members from angiosperms have been found on the
PM at steady state (Marmagne et al., 2004; Uemura
et al., 2004). The VAMP727-like proteins of the seed
plants have a common 20-residue insertion in the
N-terminal domain that distinguishes these proteins
from the other VAMP72 proteins (Supplemental Fig.
S8). The split to make the VAMP724 subgroup seems
to have happened in the seed plants and perhaps in
the angiosperms, suggesting a more recent specialization of function. Importantly, together with the PM
syntaxins, this parallel enlargement of the VAMP72
group seems to have occurred during the time of the
rise of complex multicellularity among the green plant
lineage (Fig. 5), and suggests that specializations
among the secretory machinery may have played an
essential role in the rise of multicellularity.
The Strange Case of Qb 1 Qc-SNAREs (SNAP25 Like)
SNAP25, a protein with two tandem SNARE domains (an N-terminal Qb and a C-terminal Qc domain)
was one of the original proteins to be defined as a
SNARE, and is also a member of the prototypical
SNARE complex of the mammalian synapse (for review, see Hong, 2005). In SNAP25, a stretch of Cys
residues following the N-terminal Qb-SNARE domain
are palmitoylated vivo and serve to increase the membrane interactions of these proteins (Gonzalo et al.,
1999). A third protein, SNAP29, is also found in
mammalian cells, and is thought to be involved in
similar fusion events among endosomal membranes
(Steegmaier et al., 1998). A fourth type of Qb 1 QcSNARE, SNAP47, has recently been identified in
mammals (Holt et al., 2006). Fungi also have a Qb 1
Qc-SNARE, Sec9p, which operates in the secretory
SNARE complex similar to SNAP25 in their cells (for
review, see Burri and Lithgow, 2004). Though the
fungal proteins are highly divergent from their animal
equivalents, it is generally thought that they are each
derived from a common ophistokont ancestor.
Among the green plants, the SNAP33-type proteins
are another example of a Qb 1 Qc-SNARE and have
been shown to play similar roles to that of the mammalian SNAP25. SNAP33-like proteins have been
shown to be essential in such roles as general secretion
(Kargul et al., 2001), pathogen defense (Collins et al.,
2003), and for cell plate formation during cytokinesis
12
Plant Physiol. Vol. 144, 2007
Downloaded from on June 16, 2017 - Published by www.plantphysiol.org
Copyright © 2007 American Society of Plant Biologists. All rights reserved.
The SNARE Proteins of Green Plants
Figure 4. R-SNAREs of the VAMP7 group have
greatly expanded in the land plants. Full-length
protein sequences of the R-VAMP7 orthologs
from various organisms were aligned by
ClustalW, distances were estimated with a neighbor-joining algorithm and visualized in a phylogram (top). The tree was rooted using the VAMP7
SNAREs from heterokonts. Bootstrap support is
indicated to the left of branches. The ubiquitous
VAMP71 and the green-plant-specific VAMP72
clades are indicated at right, along with the
subclades of the land plants (see text and Supplemental Fig. S8). See Figure 1 for species abbreviations.
(Heese et al., 2001). Searches in the sequences of other
green plants have identified proteins similar to
SNAP33 in gymnosperms and mosses (Fig. 2), indicating that these proteins have been in green plants
since the adaptation to land. Compared to SNAP25,
the land plant SNAP33 proteins have an N-terminal
extension (that does not bear any strong resemblance
to the N-terminal extensions of SNAP29, SNAP47, or
Sec9p), and lack the palmitoylation site of the
SNAP25-like proteins. Outside of the land plants, the
chlorophyte algae Chlamydomonas and Volvox also
encode SNAP25-like proteins (SNAP34). Oddly
enough, these proteins have an N-terminal extension
similar to that of the land plant SNAP33, yet these
proteins also have a Cys-rich sequence after the Qb-
SNARE domain similar to the sequence that is palmitoylated in SNAP25 (A. Sanderfoot, unpublished
data). Whether this domain is palmitoylated in these
algae has not been tested. The prasinophyte green
algae Ostreococcus, two thermoacidophilic red algae
(Cyanidioschyzon and Galdieria), and all the heterokonts
examined do not have any SNAP25-like SNAREs
(Table I; Fig. 2).
Since the divergence between the animal and fungi
and green plant lineages span the many SNAP25lacking unicellular protist groups (Table I; Dacks and
Doolittle, 2001), the presence of this gene in these disparate branches is difficult to reconcile by strict parsimony. Furthermore, that Chlamydomonas and Volvox
could have a Qb 1 Qc-SNARE that is palmitoylated
Plant Physiol. Vol. 144, 2007
13
Downloaded from on June 16, 2017 - Published by www.plantphysiol.org
Copyright © 2007 American Society of Plant Biologists. All rights reserved.
Sanderfoot
Figure 5. Hypothetical expansion of
secretory SNARE gene families in the
green plants. Relevant taxa of green
plants are indicated with boxes representing the hypothesized state of the
Qa-SYP1 and R-VAMP7 gene families
at the point in green plant evolution
indicated by the arrow. New gene
families are indicated by indented
names with arrows indicating the hypothetical descent of that gene from a
related gene family (see text and Supplemental Figs. S7 and S8 for more
details).
at a remarkably similar sequence to that of the vertebrate SNAP25 proteins is strange, especially considering that this trait is not shared with organisms within
their separate lineages. Did the green plants invent
SNAP33 distinct from the animals and fungi, or have
many other lineages lost the ancestral gene retained
in the plants, animals, and fungi. Finally, considering
the essential role of SNAP25-like proteins in the secretory process of those cells that possess them, what
SNAREs have replaced SNAP25 in those eukaryotes
that lack this class of SNARE?
Additional SNAREs First Identified in Plants: Qb-NPSN1
and Qc-SYP7
Through searches in the genomic sequence of the
model plant Arabidopsis, new types of Qb- and QcSNAREs that were not found in animal or fungal
genomes were identified (Sanderfoot et al., 2000). As
more sequence information later became available
from nonanimal/fungal unicellular eukaryotes, homologs of SYP7 and NPSN have turned up in alveolates, chromists/heterokonts, and amoebae, though
never in an animal or fungi (Table I; Fig. 2; Supplemental Figs. S3 and S4). Since these proteins do not
exist in the heavily studied animal or fungal systems,
they did not receive as much attention as other types of
SNAREs, but recent work has begun to indicate that
these proteins may be worthy of more study.
Outside of green plants, these types of Qb- and QcSNAREs are found in most eukaryotes that lack the
Qb 1 Qc-SNAP25-type SNARE that seems to be involved in secretion (see above). This leads to the hypothesis that these SNAREs have replaced (or were
replaced by) SNAP25-like SNAREs in secretion/exocytosis in these important groups of eukaryotes. Evidence for a role in secretion comes from experiments
in the angiosperm Arabidopsis where it has been
shown that Qb-NSPN11 and Qc-SYP71 interact with
the cell-plate-specific Qa-KNOLLE, and have a role in
Table II. Web sites of genome assemblies used in this work
Green Plants
Genome Assembly Sites
Arabidopsis v6.0
Rice v4.0
Poplar v1.0
Chlamydomonas v3.0
Volvox v0.0
O. tauri v2.0
O. lucimarinus v2.0
P. patens v1.0
Red algae
C. merolae v1.0
Galdieria sulfuraria v0.0
Heterokonts
T. pseudonana v1.0
P. tricornutum v1.0
P. sojae v1.1
P. ramorum v1.1
www.arabidopsis.org
http://www.tigr.org/tdb/e2k1/osa1/
http://genome.jgi-psf.org/Poptr1/Poptr1.home.html
http://genome.jgi-psf.org/Chlre3/Chlre3.home.html
(not publicly released, available through JGI Chlamydomonas site)
http://genome.jgi-psf.org/Ostta4/Ostta4.home.html
http://genome.jgi-psf.org/Ost9901_3/Ost9901_3.home.html
http://genome.jgi-psf.org/Phypa1/Phypa1.home.html
http://merolae.biol.s.u-tokyo.ac.jp/
http://genomics.msu.edu/galdieria/about.html
http://genome.jgi-psf.org/thaps1/thaps1.home.html
http://genome.jgi-psf.org/Phatr1/Phatr1.home.html
http://genome.jgi-psf.org/Physo1_1/Physo1_1.home.html
http://genome.jgi-psf.org/Phyra1_1/Phyra1_1.home.html
14
Plant Physiol. Vol. 144, 2007
Downloaded from on June 16, 2017 - Published by www.plantphysiol.org
Copyright © 2007 American Society of Plant Biologists. All rights reserved.
The SNARE Proteins of Green Plants
the secretion-related process of cytokinesis (Zheng
et al., 2003; L. Conner and A. Sanderfoot, unpublished
data). Moreover, these proteins are found on various
organelles in the late secretory system in nondividing
cells (Zheng et al., 2003; Marmagne et al., 2004;
Mongrand et al., 2004; Morel et al., 2006). When
members of the Qc-SYP7 group were fused to a
fluorescent protein and overexpressed in protoplasts,
these fusion proteins were reported to localize to the
ER (Uemura et al., 2004). This result is at odds with the
results of others when examining tobacco (Nicotiana
tabacum) cells (Marmagne et al., 2004; Mongrand et al.,
2004; Morel et al., 2006). Whether this result is simply
an overexpression artifact or a reflection of a specialized role for these proteins under certain conditions
remains to be seen. Still, it seems possible that these
proteins may be the major mediators of secretion in
organisms that lack SNAP25-like Qb 1 Qc-SNAREs,
which includes many medically relevant organisms
like the unicellular pathogens and parasites. Obviously, this requires more work in both plants and in
other nonanimal/fungal eukaryotes, where the mechanical aspects of secretion have not been thoroughly
investigated. Meanwhile, as an additional set of secretory Qb- and Qc-SNAREs in the green plant lineage
(along with the Qb 1 Qc-SNAP33 group), they provide an additional flexibility for the SNARE complexes
that can mediate secretory vesicle trafficking, and thus
can be considered to be part of the enlarged complement of secretory SNAREs among the multicellular
green plants.
CONCLUSION
The SNARE family of proteins has greatly enlarged
among the land plants with respect to their unicellular
ancestors. This is apparent in Figures 1 and 2, as well
as in the ordered list of SNAREs for each organism
given in Supplemental Table S1. The chlorophyte
algae, perhaps representing the state of unicellular
green plants, have the basic core of the eukaryotic
SNARE proteins among their 30 to 35 SNARE-encoding
genes. The moss Physcomitrella, arguably representing the state of the first land plants, increases the
number of SNAREs to a total of 63 that represent
almost all of the major groups and subgroups of the
angiosperm SNAREs. Among the angiosperms, the
numbers of SNAREs vary from 62 to 76 with only a
small number of new groups with respect to the
mosses. Clearly, the doubling of SNARE-encoding
genes that occurs between the chlorophyte algae and
the mosses spans several morphological innovations.
The observation that most of these new SNAREs are
related to secretory function, and the importance of a
specialized secretory pathway in multicellular organisms, it seems reasonable to hypothesize that this
increase in SNARE number is related to multicellularity. Others have made this suggestion in the past, both
in relation to the green plants and the animals (Dacks
and Doolittle, 2002, 2004), and the increased genomic
information available today has supported and extended this hypothesis. Other lineages, such as some
groups of red algae and the brown algal kelps, have
also undergone well-documented transitions to multicellularity from unicellular ancestors. Unfortunately,
there is no genome sequence currently available from
these groups to test if a comparable expansion of
SNARE proteins is found among these multicellular
eukaryotes. Additional sequence information may one
day be available from representatives of multicellular
brown and red algae, as well as some of the charophyte ancestors of plants. Such data may provide more
evidence on the link between SNAREs and multicellularity in the near future.
Even with eight green plants, we have only examined the tips of plant diversity, and many evolutionarily significant green plants are not yet available to be
examined. In the next few years, three relatives of
Arabidopsis (Arabidopsis lyrata, Capsella rubella, and
Thellungiella halophila), fabids like Medicago truncatula,
and asterids like monkey flower (Mimulus) and tomato
(Solanum lycopersicum) will become available for more
thorough examination of the dicot SNARE gene families. There will also be several grass and nongrass
monocots available soon to better define the angiosperm clades, as well as the lycophyte Selaginella
moellendorffii to aid in broader comparisons among
the basal plants. Based upon the relatively small
differences between the already available angiosperms
and moss, there may not be great differences in the
final numbers of SNAREs revealed in these plants, but
each may help to narrow down the appearance of
particular gene families and better define how each
has helped to establish the unique aspects of the very
successful green plant lineage.
MATERIALS AND METHODS
Sequence Databases
The genome assemblies searched for this work are listed in Table II. In
addition to the green plant sequences, SNAREs were also examined in several
other nongreen plant algae for whom sequence assemblies were available (see
Supplemental Table S1). The Volvox assembly has not been publicly released, but
can be accessed by searches through the Joint Genome Institute (JGI) Chlamydomonas site. The plant gene indices (currently available through the Dana
Farber Computational Biology and Functional Genomics portal: http://compbio.
dfci.harvard.edu/tgi/) were also used to identify ESTs for several related or
taxonomically relevant plants. Though ESTs will definitely underestimate the
number of SNAREs in a given organism, the encoded protein sequences were
often useful for preventing long-branch issues (barley [Hordeum vulgare] as a
second representative of grasses), and for bridging gaps in the evolutionary
series (loblolly pine [Pinus taeda] for the gymnosperms). All other sequences
were acquired from GenBank accessions of the respective assemblies. The
tables and figures in this work refer to either the unique protein ID of the
organism-specific genome databases (see Table II), or to a GenBank accession.
Searches and Annotations
The seed used for searches was the annotated list of Arabidopsis
(Arabidopsis thaliana) SNAREs kept by the author based upon prior work
(Sanderfoot et al., 2000; Pratelli et al., 2004; Sutter et al., 2006), as well as
Plant Physiol. Vol. 144, 2007
15
Downloaded from on June 16, 2017 - Published by www.plantphysiol.org
Copyright © 2007 American Society of Plant Biologists. All rights reserved.
Sanderfoot
information from other similar works (Bock et al., 2001; Hong, 2005; Yoshizawa
et al., 2006) and unpublished information. These proteins were used to
iteratively search through the genome databases using BLASTp, tBLASTn,
and related searches (including keyword searches of autoannotations when
possible) to assure that all possible SNARE-encoding genes were identified in
the databases. When possible, EST information was used to confirm exon
structure, otherwise the best possible model was chosen for each gene based
upon homology with a related genome sequence (either an internal paralog or
a homolog in a related organism). Each predicted SNARE protein was
iteratively compared (by BLASTp or PSI-BLAST) to the nonredundant protein
database at the National Center for Biotechnology Information (http://
www.ncbi.nlm.nih.gov), the predicted proteins of the individual genome
assemblies (including that of the source organism to identify gene family
members and help identify pseudogenes and poor gene predictions), the
Conserved Domain Database (http://www.ncbi.nlm.nih.gov/Structure/
cdd/cdd.shtml), and the KOGnitor (http://www.ncbi.nlm.nih.gov/COG/
grace/kognitor.html). Through such analysis, typically a single group of
SNAREs (e.g. a KOG) was identified as the most likely candidate based upon a
highly significant score (greater than 1e-20), and a significant distinction from
other groups. In cases where such a KOG (or other similar group) was not
identified, a temporary group was created to facilitate identification of groups
that lie outside the previously established groups. Finally, each protein was
subjected to phylogenetic analysis with members of well-known SNARE
groups (i.e. Sanderfoot et al., 2000; Bock et al., 2001; Pratelli et al., 2004) to
ensure that the assignment of the particular SNARE group based upon the
profile-based searches is consistent with the well-known phylogeny. As new
genome information was added, each subsequent set of predicted SNARE
proteins was added to the analysis until the groups indicated in this work
were apparent.
Because this work was based upon the information present in the genome
assemblies, it was common to identify poor gene predictions based upon the
automated gene prediction algorithms. Some of these predictions could be
fixed by additional cDNA/EST information, by changing to a different algorithm model, or making adjustments to the model in attempts to create a gene
prediction with a typical SNARE structure (through addition or adjustments
to exons). In some cases, this was not possible, and the most likely predictions
appeared to be fragmentary genes, or pseudogenes. Gene fragments and
pseudogenes represent cases where the most similar sequence (both protein
and nucleotide) would be from a related gene in the same genome, but
the predicted gene would only represent a truncated protein or a protein
that would be missing functionally relevant domains found in SNARE
proteins. In this analysis, none of the predicted gene fragments had any
evidence of expression. Some pseudogenes are represented in EST databases,
but in many cases this expression was very limited. For example, Arabidopsis
VAMP723 (At2g33110) contains several mutations in the third exon (with
respect to other gene family members; this exon encodes the conserved central
core of the SNARE motif), and has evidence of only very low expression across
many tissues (as derived from AtGenExpress data; Schmid et al., 2005). Even if
such a protein were produced, it would be very unlikely to produce a
functional SNARE protein. Although such genes were included in Supplemental Table S1, they were generally not used in phylogenetic analysis since
pseudogenes and gene fragments can significantly affect alignment and
distance estimates.
Alignment and Phylogeny
The SNARE protein sequences, either full length or just the SNARE
domain were aligned by ClustalW (MEGA3.1 software; Kumar et al., 2004).
Alignments of only the SNARE domains were created by hand through
deletion of all residues except the traditionally defined heptad-repeat motif
common to all SNAREs. Trees were produced using a boot-strapped neighborjoining algorithm (Saitou and Nei, 1987; as implemented in MEGA3.1) using
standard settings. Other methods of phylogenetic analysis did not result in
any significant changes to topology identified by neighbor joining (data not
shown), nor did such methods help to resolve some poorly supported
branches. Among the green plant sequences, very little change in topology
occurred between analyses using full-length sequences and those using just
the SNARE domain. The latter were only used in cases where truncated
SNAREs (brevins, or the BET1/SFT1 groups) that lack the N-terminal extensions were the object of study to prevent spurious alignments and in cases
where all-SNARE alignments were used to allow useful distance estimations.
Examination of the gene structure (intron position and number, etc.) for
several SNARE groups also helped support some weakly supported clusters.
Other information, such as the well-established evolutionary series or green
plants and algae (e.g. Sanderson et al., 2004) also helped to support some of
the phylogenetic analysis.
Supplemental Data
The following materials are available in the online version of this article.
Supplemental Figure S1. Phylogenetic tree of ER Qb- and Qc-SNAREs.
Supplemental Figure S2. Phylogenetic tree of Qa-SNAREs from five
major clades.
Supplemental Figure S3. Phylogenetic tree of Qb-SNAREs of the Golgi,
endosomes, and PM.
Supplemental Figure S4. Phylogenetic tree of Qc-SNAREs of the TGN,
endosomes, and PM.
Supplemental Figure S5. Phylogenetic tree of Brevin-like Qc-SNAREs.
Supplemental Figure S6. Phylogenetic tree of Longin-type R-SNAREs.
Supplemental Figure S7. Alignment of Qa-SYP1 SNAREs.
Supplemental Figure S8. Alignment of R-VAMP7 SNAREs.
Supplemental Table S1. List of predicted SNARE proteins from green
plant genomes.
ACKNOWLEDGMENTS
The author acknowledges the assistance of lab members Laura Conner
and Lingtian Kong in reading and commenting on the manuscript, as well as
the Chlamydomonas and Physcomitrella genome sequence projects for allowing
me to take part in the genome annotation process for those organisms. I also
appreciate the resources made available by the Department of Energy Joint
Genome Institute for genome annotation and analysis that were helpful in
preparation of this manuscript.
Received November 14, 2006; accepted March 6, 2007; published March 16,
2007.
LITERATURE CITED
Adl SM, Simpson AG, Farmer MA, Andersen RA, Anderson OR, Barta
JR, Bowser SS, Brugerolle G, Fensome RA, Fredericq S, et al (2005) The
new higher level classification of eukaryotes with emphasis on the
taxonomy of protists. J Eukaryot Microbiol 52: 399–451
Assaad FF, Qiu JL, Youngs H, Ehrhardt D, Zimmerli L, Kalde M, Wanner
G, Peck SC, Edwards H, Ramonell K, et al (2004) The PEN1 syntaxin
defines a novel cellular compartment upon fungal attack and is required
for the timely assembly of papillae. Mol Biol Cell 15: 5118–5129
Bassham DC, Sanderfoot AA, Kovaleva V, Zheng H, Raikhel NV (2000)
AtVPS45 complex formation at the TGN. Mol Biol Cell 11: 2251–2265
Bock JB, Matern HT, Peden AA, Scheller RH (2001) A genomic perspective
on membrane compartment organization. Nature 409: 839–841
Burri L, Lithgow T (2004) A complete set of SNAREs in yeast. Traffic 5:
45–52
Carter C, Pan S, Zouhar J, Avila EL, Girke T, Raikhel NV (2004) The
vegetative vacuole proteome of Arabidopsis thaliana reveals predicted
and unexpected proteins. Plant Cell 16: 3285–3303
Catalano CM, Czymmek KJ, Gann JG, Sherrier DJ (2007) Medicago
truncatula syntaxin SYP132 defines the symbiosome membrane and
infection droplet membrane in root nodules. Planta 225: 541–550
Cavalier-Smith T (1998) A revised six-kingdom system of life. Biol Rev
Camb Philos Soc 73: 203–266
Chatre L, Brandizzi F, Hocquellet A, Hawes C, Moreau P (2005) Sec22
and Memb11 are v-SNAREs of the anterograde endoplasmic reticulumGolgi pathway in tobacco leaf epidermal cells. Plant Physiol 139:
1244–1254
Chen Y, Shin YK, Bassham DC (2005) YKT6 is a core constituent of
membrane fusion machineries at the Arabidopsis trans-Golgi network.
J Mol Biol 350: 92–101
Collins NC, Thordal-Christensen H, Lipka V, Bau S, Kombrink E, Qiu JL,
Huckelhoven R, Stein M, Freialdenhoven A, Somerville SC, et al
16
Plant Physiol. Vol. 144, 2007
Downloaded from on June 16, 2017 - Published by www.plantphysiol.org
Copyright © 2007 American Society of Plant Biologists. All rights reserved.
The SNARE Proteins of Green Plants
(2003) SNARE-protein-mediated disease resistance at the plant cell wall.
Nature 425: 973–977
Dacks JB, Doolittle WF (2001) Reconstructing/deconstructing the earliest
eukaryotes: how comparative genomics can help. Cell 107: 419–425
Dacks JB, Doolittle WF (2002) Novel syntaxin gene sequences from
Giardia, Trypanosoma and algae: implications for the ancient evolution of the eukaryotic endomembrane system. J Cell Sci 115:
1635–1642
Dacks JB, Doolittle WF (2004) Molecular and phylogenetic characterization of syntaxin genes from parasitic protozoa. Mol Biochem Parasitol
136: 123–136
Geelen D, Leyman B, Batoko H, Di Sansebastiano GP, Moore I, Blatt MR
(2002) The abscisic acid-related SNARE homolog NtSyr1 contributes to
secretion and growth: evidence from competition with its cytosolic
domain. Plant Cell 14: 387–406
Gonzalo S, Greentree WK, Linder ME (1999) SNAP-25 is targeted to the
plasma membrane through a novel membrane-binding domain. J Biol
Chem 274: 21313–21318
Heese M, Gansel X, Sticher L, Wick P, Grebe M, Granier F, Jürgens G
(2001) Functional characterization of the KNOLLE-interacting t-SNARE
AtSNAP33 and its role in plant cytokinesis. J Cell Biol 155: 239–249
Holt M, Varoqueaux F, Wiederhold K, Takamori S, Urlaub H, Fasshauer
D, Jahn R (2006) Identification of SNAP-47, a novel Qbc-SNARE with
ubiquitous expression. J Biol Chem 281: 17076–17083
Hong W (2005) SNAREs and traffic. Biochim Biophys Acta 1744: 120–144
Lauber MH, Waizenegger I, Steinmann T, Schwarz H, Mayer U, Hwang I,
Lukowitz W, Jürgens G (1997) The Arabidopsis KNOLLE protein is a
cytokinesis-specific syntaxin. J Cell Biol 139: 1485–1493
Lopez-Bautista JM, Waters DA, Chapman RL (2003) Phragmoplastin,
green algae and the evolution of cytokinesis. Int J Syst Evol Microbiol 53:
1715–1718
Lukowitz W, Mayer U, Jürgens G (1996) Cytokinesis in the Arabidopsis
embryo involves the syntaxin-related KNOLLE gene product. Cell 84:
61–71
Kargul J, Gansel X, Tyrrell M, Sticher L, Blatt MR (2001) Protein-binding
partners of the tobacco syntaxin NtSyr1. FEBS Lett 508: 253–258
Kumar S, Tamura K, Nei M (2004) MEGA3: integrated software for
molecular evolutionary genetics analysis and sequence alignment. Brief
Bioinform 5: 150–163
Mallard F, Tang BL, Galli T, Tenza D, Saint-Pol A, Yue X, Antony C, Hong
W, Goud B, Johannes L (2002) Early/recycling endosomes-to-TGN
transport involves two SNARE complexes and a Rab6 isoform. J Cell
Biol 156: 653–664
Marmagne A, Rouet MA, Ferro M, Rolland N, Alcon C, Joyard J, Garin J,
Barbier-Brygoo H, Ephritikhine G (2004) Identification of new intrinsic
proteins in Arabidopsis plasma membrane proteome. Mol Cell Proteomics 3: 675–691
Mongrand S, Morel J, Laroche J, Claverol S, Carde JP, Hartmann MA,
Bonneu M, Simon-Plas F, Lessire R, Bessoule JJ (2004) Lipid rafts in
higher plant cells: purification and characterization of Triton X-100insoluble microdomains from tobacco plasma membrane. J Biol Chem
279: 36277–36286
Morel J, Claverol S, Mongrand S, Furt F, Fromentin J, Bessoule JJ, Blein
JP, Simon-Plas F (2006) Proteomics of plant detergent-resistant membranes. Mol Cell Proteomics 5: 1396–1411
Muller I, Wagner W, Volker A, Schellmann S, Nacry P, Kuttner F,
Schwarz-Sommer Z, Mayer U, Jurgens G (2003) Syntaxin specificity
of cytokinesis in Arabidopsis. Nat Cell Biol 5: 531–534
Mullock BM, Smith CW, Ihrke G, Bright NA, Lindsay M, Parkinson EJ,
Brooks DA, Parton RG, James DE, Luzio JP, et al (2000) Syntaxin 7
is localized to late endosome compartments, associates with Vamp 8,
and is required for late endosome-lysosome fusion. Mol Biol Cell 11:
3137–3153
Nühse TS, Boller T, Peck SC (2003) A plasma membrane syntaxin is
phosphorylated in response to the bacterial elicitor flagellin. J Biol Chem
278: 45248–45254
Parlati F, Varlamov O, Paz K, McNew JA, Hurtado D, Sollner TH,
Rothman JE (2002) Distinct SNARE complexes mediating membrane
fusion in Golgi transport based on combinatorial specificity. Proc Natl
Acad Sci USA 99: 5424–5429
Pratelli R, Sutter JU, Blatt MR (2004) A new catch in the SNARE. Trends
Plant Sci 9: 187–195
Pryor PR, Mullock BM, Bright NA, Lindsay MR, Gray SR, Richardson
SC, Stewart A, James DE, Piper RC, Luzio JP (2004) Combinatorial
SNARE complexes with VAMP7 or VAMP8 define different late endocytic fusion events. EMBO Rep 5: 590–595
Rancour DM, Dickey CE, Park S, Bednarek SY (2002) Characterization of
AtCDC48: evidence for multiple membrane fusion mechanisms at the
plane of cell division in plants. Plant Physiol 130: 1241–1253
Rojo E, Gillmor CS, Kovaleva V, Somerville CR, Raikhel NV (2001)
VACUOLELESS1 is an essential gene required for vacuole formation
and morphogenesis in Arabidopsis. Dev Cell 1: 303–310
Rojo E, Zouhar J, Kovaleva V, Hong S, Raikhel NV (2003) The AtC-VPS
protein complex is localized to the tonoplast and the prevacuolar
compartment in Arabidopsis. Mol Biol Cell 14: 361–369
Rossi V, Banfield DK, Vacca M, Dietrich LE, Ungermann C, D’Esposito M,
Galli T, Filippini F (2004) Longins and their longin domains: regulated
SNAREs and multifunctional SNARE regulators. Trends Biochem Sci 29:
682–688
Saitou N, Nei M (1987) The neighbor-joining method: a new method for
reconstructing phylogenetic trees. Mol Biol Evol 4: 406–425
Sanderfoot AA, Assaad FF, Raikhel NV (2000) The Arabidopsis genome:
an abundance of SNAREs. Plant Physiol 124: 1558–1569
Sanderfoot AA, Kovaleva V, Bassham DC, Raikhel NV (2001) Interactions
between syntaxins identify at least five SNARE complexes within the
Golgi/prevacuolar system of the Arabidopsis cell. Mol Biol Cell 12:
3733–3743
Sanderson MJ, Thorne JL, Wikström N, Bremer K (2004) Molecular
evident on plant divergence times. Am J Bot 91: 1656–1665
Schmid M, Davison TS, Henz SR, Pape UJ, Demar M, Vingron M,
Scholkopf B, Weigel D, Lohmann JU (2005) A gene expression map of
Arabidopsis thaliana development. Nat Genet 37: 501–506
Steegmaier M, Yang B, Yoo JS, Huang B, Shen M, Yu S, Luo Y, Scheller RH
(1998) Three novel proteins of the syntaxin/SNAP-25 family. J Biol
Chem 273: 34171–34179
Sun W, Yan Q, Vida TA, Bean AJ (2003) Hrs regulates early endosome
fusion by inhibiting formation of an endosomal SNARE complex. J Cell
Biol 162: 125–137
Sutter JU, Campanoni P, Blatt MR, Paneque M (2006) Setting SNAREs in a
different wood. Traffic 7: 627–638
Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV,
Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN, et al (2003)
The COG database: an updated version includes eukaryotes. BMC
Bioinformatics 4: 41
Uemura T, Ueda T, Ohniwa RL, Nakano A, Takeyasu K, Sato MH (2004)
Systematic analysis of SNARE molecules in Arabidopsis: dissection of
the post-Golgi network in plant cells. Cell Struct Funct 29: 49–65
Volchuk A, Ravazzola M, Perrelet A, Eng WS, Di Liberto M, Varlamov O,
Fukasawa M, Engel T, Sollner TH, Rothman JE, et al (2004) Countercurrent distribution of two distinct SNARE complexes mediating transport within the Golgi stack. Mol Biol Cell 15: 1506–1518
Ward DM, Pevsner J, Scullion MA, Vaughn M, Kaplan J (2000) Syntaxin 7
and VAMP-7 are soluble N-ethylmaleimide-sensitive factor attachment
protein receptors required for late endosome-lysosome and homotypic
lysosome fusion in alveolar macrophages. Mol Biol Cell 11: 2327–2333
Yano D, Sato M, Saito C, Sato MH, Morita MT, Tasaka M (2003) A SNARE
complex containing SGR3/AtVAM3 and ZIG/VTI11 in gravity-sensing
cells is important for Arabidopsis shoot gravitropism. Proc Natl Acad
Sci USA 100: 8589–8594
Yoshizawa AC, Kawashima S, Okuda S, Fujita M, Itoh M, Moriya Y,
Hattori M, Kanehisa M (2006) Extracting sequence motifs and the
phylogenetic features of SNARE-dependent membrane traffic. Traffic 7:
1104–1118
Zheng H, Bednarek SY, Sanderfoot AA, Alonso J, Ecker JR, Raikhel NV
(2003) NPSN11 is a cell plate associated SNARE protein that interacts
with the syntaxin KNOLLE. Plant Physiol 129: 530–539
Plant Physiol. Vol. 144, 2007
17
Downloaded from on June 16, 2017 - Published by www.plantphysiol.org
Copyright © 2007 American Society of Plant Biologists. All rights reserved.