Article Figures & Data
Figures
- Figure 1.
Distribution pattern of Arabidopsis and yeast kinase reveals lack of RLK and Raf-like MAP3K in yeast. The tree displays the phylogenetic relationship between the 12 conventional protein kinase clusters shown in Table II. Each branch represents a cluster described in Table II. A branch length unit corresponds to a 10-fold difference in BLAST E value. Arabidopsis-specific clusters are denoted by a white triangle. Each branch is labeled with the cluster number followed by the number of Arabidopsis (A.t.) and yeast (S.c.) kinases in the cluster. Each non-RLK cluster is briefly annotated, and the corresponding figure number is identified when a cluster is displayed later.
- Figure 2.
Arabidopsis lacks homologs for yeast provirus insertion in mouse (PIM)-like, Ca2+/calmodulin-dependent protein kinase (CaMK), NPR/HAL5, polyamine transport kinase (PTK), and RAN kinase families. The tree displays cluster 7 and is extensively compressed at family level due to the large number of proteins included. The black triangle branch denotes subcluster of multiple kinases. Yeast- and Arabidopsis-specific subcluster are denoted by one asterisk and two asterisks, respectively. Some of the compressed subclusters are shown later (see Figs. 7, 8, 9, 10, 11), and corresponding figure numbers are identified. A black diamond denotes branch representing a yeast kinase. Corresponding yeast kinase families and groups are labeled at the right end of the tree.
- Figure 6.
Arabidopsis preserves the phospho-relay signaling mechanism. The tree of His kinases is displayed. Branch representing a yeast kinase is denoted by a black diamond and text following an Arabidopsis gene identification, when present, represents name previously assigned to the kinase. Subclusters, when corresponding to a functional group, are labeled at the right end of the tree in blue text.
- Figure 7.
Trees of MAP3K (a) and STE20-like/MAP4K kinases (b). These are subclusters from the tree shown in Figure 2. Branch representing a yeast kinase is denoted by a black diamond and name(s) previously assigned to an Arabidopsis kinase through experimental characterization, when present, follow an Arabidopsis gene identification.
- Figure 11.
The trees of GSK3/Shaggy-like kinase family (a) and Casein kinase II family (b). It represents a subcluster from the tree shown in Figure 2. A black diamond denotes branch representing a yeast kinase. Name(s) previously assigned to an Arabidopsis kinase through experimental characterization, when present, follow an Arabidopsis gene identification. The shaded box identified protein kinases with significant mutual E values (clustered together to the right of the vertical line indicating a BLAST E value of 10-80, see Fig. 2).
- Figure 3.
Arabidopsis lacks obvious orthologs to PKA and PKC but preserves and sometimes expands other kinase family of the yeast kinase group AGC. The tree displays cluster 8. Branch representing a yeast kinase is labeled with a black diamond, and the corresponding yeast kinase families are labeled at the right end of the tree. The shaded box identified protein kinases with significant mutual E values (clustered together to the right or near left of the vertical line indicating a BLAST E value of 10-80).
- Figure 4.
Expansion of the yeast casein kinase I family member HRR25 and CLK kinase family in Arabidopsis. The tree displays cluster 9. A black diamond denotes a branch representing a yeast kinase, and the corresponding yeast kinase families are labeled at the right end of the tree. Name(s) previously assigned to an Arabidopsis kinase through experimental characterization, when present, follow an Arabidopsis gene identification. The shaded box identified protein kinases with significant mutual E values (clustered together to the right of the vertical line indicating a BLAST E value of 10-80).
- Figure 5.
Relative distribution of yeast and Arabidopsis kinases in clusters 11 and 12. The trees for the two clusters are shown in a and b, respectively, with the yeast gene denoted with a black diamond. Name(s) previously assigned to an Arabidopsis kinase through experimental characterization, when present, follow an Arabidopsis gene identification. The shaded box identified protein kinases with significant mutual E values (10-92).
- Figure 8.
Trees of MAP2Ks (a) and MAPKs (b). These are subclusters from the tree shown in Figure 2. Branch representing a yeast kinase is denoted by a filled diamond and name(s) previously assigned to an Arabidopsis kinase through experimental characterization, when present, follow an Arabidopsis gene identification.
- Figure 9.
Expansion of the yeast kinase SNF1 in Arabidopsis. The tree of SnRKs is displayed. It represents a subcluster from the tree shown in Figure 2. Branch representing a yeast kinase is denoted by a black diamond, and name(s) previously assigned to an Arabidopsis kinase through experimental characterization, when present, follow an Arabidopsis gene identification. The shaded box identified protein kinases with significant mutual E values (clustered together to the right of the vertical line indicating a BLAST E value of 10-80).
- Figure 10.
The tree of cyclin-dependent protein kinases (CDKs). It represents a subcluster from the tree shown in Figure 2. Branch representing a yeast kinase is denoted by a black diamond, and name(s) previously assigned to an Arabidopsis kinase through experimental characterization, when present, follow an Arabidopsis gene identification. The shaded box identified protein kinases with significant mutual E values (clustered together to the right or near left of the vertical line indicating a BLAST E value of 10-80).
Tables
Type Cluster Representative Family PlantsP Classification No. No. of Arabidopsis Genes No. of Yeast Genes Receptor-like kinases (RLKs) and related kinase 1 N/Sa N/S 497 0 2 N/S N/S 67 0 3 N/S N/S 54 0 4 N/S N/S 4 0 Intracellular kinase 5 Raf-like MAP3K 2.1.3-4 22 0 AtMRK1/ATN1 like 2.1.5-6 26 0 Ankyrin repeat kinase 2.1.2 6 0 6 MEKK/NPK1 like 4.4.1-5 26 0 7 APG1 like 4.2.8 4 1 ELM 4.2.7 2 3 SnRK (SNF1 like) 4.2.4 38 9 CDPK 4.2.1, 4.2.3 40 0 PPCK 4.2.2 4 0 CaMK N/Ab 0 6 MAP4K/STE20 like 4.1.2 9 5 MAP3K 4.1.1 12 5 MAP2K 4.1.3-4 10 4 MAPK 4.5.1 19 6 Casein kinase II 4.5.3 4 2 CDK 4.5.2 27 5 GSK3/shaggy like 4.5.4 10 4 NIMA/NEK family 4.1.6 7 1 CLK 4.5.1 3 1 (of 4) PIM like N/A 0 2 RAN N/A 0 2 PTK N/A 0 2 NPR/HAL5 N/A 0 7 8 S6K 4.2.6 26 2 DBF2 12 3 PKA 0 3 PKC 0 1 AGC 2 3 PKA related 2 3 9 Casein kinase I 3.1.1 17 4 10 CLK 3.1.1 16 3 (of 4) 11 IRE1 4.3.2 3 1 12 5.2.1 1 (4g29380) 2 Histidine kinase 13 SLN1 0 1 Cytokinin receptor 6 0 Ethylene receptor 5 0 Phytochrome 5 0 14 PDH kinase 1 1 PI kinase like 15 PI kinase like N/A 3 2: AtATM MEC1 AtRad3 TEL1 At1g50030 Unclustered kinase N/A N/A N/A 3: 2: At1g22870 BUD32 At3g63330 TWF1 At5g53450 - Table II.
Reported functional orthologs identified through genetic complementation analysis in yeast
The list was generated through a search of National Center for Biotechnology Information PubMed for genetic complementation that occurred between a pair of protein kinases of similar signaling pathways.
Arabidopsis Gene Yeast Gene Figure Reference(s) At4g01370/AtMPK4 SLT2 8b Mizoguchi et al. (1998) At5g56580/AtMEK1 PBS2 8a At1g54960/AtANP1 STE11 7a Nishihama et al. (1997) At4g08500/AtMEKK1 Covic and Lew (1996) Mizoguchi et al. (1996) At3g48750/AtCDC2a CDC28(p34cdc2) 10 Ferreira et al. (1991) At5g24360/Atlre1-1 IRE1 5a Koizumi et al. (2001) At2g17520/Atlre1-2 At1g06390/AtGSK1 MCK1 11a Piao et al. (1999) At3g01090/Akin10 SNF1 9 Alderson et al. (1991); Bhalerao et al. (1999) At3g29160/Akin11 At2g17820/ATHK1 SLN1 6 Urao et al. (1999) - Table III.
Protein kinases of yeast and Arabidopsis that share significant mutual E values
They are identified by a shaded box in corresponding figures.
Yeast Family Yeast Gene Function (from SGD) Arabidopsis Orthologs Cluster E Value DBF2 CBK1 Pheromone response: shmooing At1g03920 10-110 At2g20470 At3g23310 At4g14350 At1g30640 At5g09890 At2g19400 At4g33080 AGC YPK1 Vegetative growth At3g08720 10-68 YPK2 At3g08730 S6K KIN82 Unknown At5g58140 10-78 YNR047W At3g45780 CK-I HRR25 DNA repair At1g03930 10-96 At5g44100 At1g04440 At5g43320 At3g23340 At4g14340 At4g28540 At1g72710 At4g26100 At2g19470 At4g28860 At4g28880 At4g08800 CLK YAK1 Complement PKA deletion At5g35980 10-98 N/A VPS15 Vacuolar transport At4g29380 10-92 SNF1 SNF1 Glc Metabolism At5g59340 10-101 At3g29160 At3g01090 CDK CDC28 G1/S and G2/M transition At3g48750 10-86 At1g20930 At1g76540 At2g38620 At3g54180 KIN28 Transcription Regulation At1g66750 10-78 At1g73690 At1g18040 GSK3 MRK1 Unknown At1g09840 10-92 At1g57870 RIM11 Meiosis At5g26750 At3g05840 At5g14640 At4g00720 At1g06390 At2g30980 At4g18710 At3g61160 CK-II CKA1 Cell cycle, cell polarity, flocculation, ion homeostasis, transcription regulation At2g23070 10-92 At2g23080 CKA2 At3g50000 At5g67380 PI kinase like MEC1 Cell cycle, DNA repair AtRAD3 10-103 TEL1 DNA repair, telomere maintenance AtATM 10-85
