Figure 1.
Vesicle transport pathways in plants.
COP-II vesicles mediate cargo transport from ER to cis-Golgi, while COP-I traffics the cargo from Golgi to ER and intra-Golgi as well. Clathrin-coated vesicles (CCVs) are involved in flow of cargo from the plasma membrane and trans-Golgi network to endosomes and retromers and ESCRTs are required for endosomal trafficking pathways. Rab GTPases are involved in regulation of vesicle formation, its uncoating and transport, while tethering factors and SNAREs facilitate the membrane fusion processes. Additionally, vesicle transport has also been discussed between other compartments (shown in grey circles- not discussed in the manuscript). The number of identified factors for COP-II, COP-I, CCVs, Retromers and ESCRTs, Rab GTPases, Tethering factors and SNAREs is shown. MIT: mitochondria, ER: endoplasmic reticulum, E: endosome, P: peroxisome, NUC: nucleus, PLAM: Plastid Associated Membranes.
Table 1.
The number of identified orthologues to COP-II-coated vesicle components.
Table 2.
The number of identified orthologues to COP-I-coated vesicle components.
Table 3.
The number of orthologues for Clathrin-Coated Vesicle (CCVs) transport factors.
Table 4.
Number of orthologues to Retromer and ESCRT transport factors.
Table 5.
The number of Rab GTPase orthologoues.
Table 6.
The orthologues of Tethering factors.
Table 7.
The number of SNARE orthologues detected.
Figure 2.
Correlation of protein sequences and orthologue number.
Shown are the number of orthologues for different vesicle transport subfamilies of yeast, A. thaliana and 13 other plant species in accordance to their phylogenetic relationship. (Scer: S. cerevisae; Crei: C. reinhardtii; Ppat: P. patens; Zmay: Z. mays; Sbic: S. bicolor; Bdis: B. distachyon; Osat: O. sativa; Stub: S. tuberosum; Slyc: S. lycopersicum; Vvin: V. vinifera; Atha: A. thaliana; Ptri: P. trichocarpa; Ljap: L. japonicus; Mtru: M. truncatula; Gmax: G. max).
Figure 3.
Classification of (co-)orthologues with different domain architecture.
(Co-)orthologues of yeast, A.thaliana and S.lycopersicum belonging to the same orthologous group but with entirely different domain structure (class III) exemplified for Sec17 (A), with additional domains when compared to the bait (class II) exemplified for COG4 and Sec26p (B) and with less domains then the bait Sec16 (C) are represented as bar diagram showing the corresponding domain architectures.
Table 8.
Chloroplast-localized vesicle transport factors.
Table 9.
Mitochondrial-localized vesicle transport factors
Figure 4.
Expression analysis of A. thaliana and S. lycopersicum genes.
Shown are the average RMA normalized expression patterns of different tissues for 10 clusters of vesicle transport factors in (A) A. thaliana and (B) S. lycopersicum. The y-axis shows the average RMA normalized expression of a maximum of 4 samples per tissue. The 10 clusters (Atha_1 to Atha_10) and (Slyc_1 to Slyc_10) were obtained by k-means clustering and split into four graphs in accordance to their expression profile in different tissues. (Leaf 3W: 3 weeks old leaf; Leaf 5W: 5 weeks old leaf).
Figure 5.
Predicted intracellular localization of factors in different clusters.
Shown are stacked bar charts of the factors categorized on the basis of consensus localization analysis. Vesicle transport factors of A. thaliana (A) and S. lycopersicum (B) are clustered concerning their tissue-specific expression and distributed to their predicted localization. The localization of A. thaliana depends on the high certainty approach. For S. lycopersicum, the localization was determined by the low certainty approach (see Materials and Methods).
Figure 6.
Putative chloroplast or mitochondrial localized vesicle transport factors.
Shown are the likely (co-)orthologues of A. thaliana (top) and the most likely factors based on the analysis of all 14 plant genomes (present in more then 7 plant genomes, bottom) which are predicted to be chloroplast (A) or mitochondrial (B) localized. The (co-)orthologues are assigned concerning the seven different vesicle transport factor families. The size of the symbol on the left size indicates the importance of the factor family.