Figure 1:.
A partial list of plant NDP-sugars and interconversion enzymes.
Eleven NDP-sugars and enzyme families involved in building plant cell wall polysaccharides are indicated. Polysaccharides in which NDP-sugars may be incorporated are indicated beside the respective NDP-sugar, underlined and italicized. Reactions are shown as arrows, and enzymes are indicated in bold beside the arrows. Abbreviations: UAXS (UDP-D-apiose/UDP-D-xylose synthase, also known as AXS), UGlcAE (UDP-D-glucuronic acid 4-epimerase, also know as GAE), GER (GDP-4-keto-6-deoxy-D-mannose-3,5-epimerase-4-reductase), GMD (GDP-D-mannose-4,6-dehydratase), GME (GDP-D-mannose 3,5-epimerase), RHM (UDP-L-rhamnose synthase), NRS/ER (nucleotide-rhamnose synthase/epimerase-reductase, also known as UER), UGD (UDP-D-glucose dehydrogenase), UGE (UDP-D-glucose 4-epimerase), UXE (UDP-D-xylose 4-epimerase) and UXS (UDP-D-xylose synthase, including AUD [membrane-anchored UXS] and SUD [soluble UXS]).
Figure 2:.
Phylogeny of 257 plant Epimerase domains.
The phylogeny is built using PhyML v3.0 and displayed using the Interactive Tree of Life (iTOL) web server (Letunic and Bork, 2007). Bootstrap values beside the nodes indicate the confidence levels with regard to the clustering of relevant proteins into one group. Selected supporting values >70% are shown. SQD1 is UDP-sulfoquinovose synthase. MAR is short for methionine adenosyltransferase regulatory protein, whose exact enzymatic function is not determined yet. CRB is short for chloroplast RNA binding. For other names, see Figure 1 for abbreviations. Note that UXS includes SUD and AUD, UGlcAE is also known as GAE, UAXS is also known as AXS and NRS/ER is also known as UER. Only sub-clades of major clade A are shown and sequence names are indicated using GenBank gi numbers or UniGene IDs. The other two clades are collapsed as black triangles. The scale bar corresponds to 0.1 changes per amino acid position. The complete version of this phylogeny is given in Figure S1.
Table 1.
Numbers of close NCBI-nr homologs of the respective plant NSE families.
Figure 3:.
Phylogeny of 44 Epimerase domains closest to plant UGlcAE proteins.
The 44 sequences are shown with GenBank gi numbers followed by species names. The phylogeny is built using both PhyML v3.0 and FastTree v2.1.1 and displayed using the Interactive Tree of Life (iTOL) web server. The topology by PhyML is shown and selected supporting values >70% from PhyML and FastTree analysis are indicated and split by ‘/’. Blue star indicates the closest bacterial homolog of plant UGlcAE proteins.
Figure 4:.
Phylogenies of 254 RHM N-terminal and 78 C-terminal domains.
A) 254 sequences closest to plant RHM N-terminal domains. The red star indicates the closest bacterial homolog of eukaryotic 4,6-dehydratases. B) 78 sequences closest to plant RHM C-terminal domains and plant NRS/ER proteins; these sequences were obtained by searching a self-built plant NRS/ER HMM against the NCBI-nr database (E-value <1e-2). The phylogenies are built using FastTree v2.1.1 and displayed using the Interactive Tree of Life (iTOL) web server. Major clades are collapsed as triangles and selected supporting values >70% are shown. Un-collapsed sequences are indicated using GenBank gi numbers followed by species names. The complete phylogenies with un-collapsed clades are given in Figures S3 and S4. C) A proposed model for the evolutionary route of the bi-domain RHMs and the single-domain 3,5-epimerase-4-reductases (NRS/ERs) in plants. The prokaryotic gene cluster is an example from Salmonella enterica serovar Typhi CT18 (Parkhill et al., 2001). Note that in different bacteria the order of the four genes could vary and some of the genes could be missing or replaced by other genes.
Figure 5:.
An evolutionary model for the origin of plant NSE families
. The ancient prokaryotes include ancient bacteria and ancient Archaea. The thick horizontal dash line indicates the time when the earliest eukaryotes emerged. The arrows show the direction of evolution.