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Supplementary Material
Exploring the evolutionary path of plant MAPK networks
Róbert Dóczi1, László Ökrész2, Alfonso E. Romero3, Alberto Paccanaro3 and László Bögre4
1Institute of Agriculture, Agricultural Research Centre of the Hungarian Academy of Sciences, Brunszvik Rd. 2, Martonvásár, H-2462, Hungary
2Institute of Plant Biology, Biological Research Center of the Hungarian Academy of Sciences, POB 521, H-6701, Szeged, Hungary
3Department of Computer Science and Centre for Systems and Synthetic Biology, Royal Holloway, University of London, Egham, TW20 0EX, UK
4School of Biological Sciences and Centre for Systems and Synthetic Biology, Royal Holloway, University of London, Egham, TW20 0EX, UK
Corresponding author: Bögre, L. ().
Table S1. MAPK and MKK sequences in green plants and in NaegleriaMAPK: TDY / MAPK: TEY / ERK8-like / MHK / MKK
Naegleria gruberi / 0 / 1 / 1 / 2 / 2
XP_002672114 / XP_002675531 / XP_002675576
XP_002679174 / XP_002675852
XP_002678931
Chlamydomonas reinhardtii / 2 / 3 / 1 / 2 / 2
XP_001703601
XP_001694300 / XP_001690852
XP_001690850
XP_001700291 / XP_001699095 / XP_001697865
XP_001693587 / XP_001696437
XP_001693665
Volvox carteri / 2 / 2 / 1 / 2 / 2
XP_002954138
XP_002954367 / XP_002955338
XP_002948304 / XP_002951120 / XP_002948753
XP_002949787 / XP_002947566
XP_002958286
Micromonas sp. / 1 / 2 / 1 / 2 / 2
XP_002503335 / XP_002503699
XP_002501054 / XP_002507666 / XP_002502211
XP_002505908 / XP_002504085
XP_002506404
Ostreococcus tauri / 1 / 2 / 0 / 0 / 1
XP_003080614 / XP_003081390
XP_003083155 / XP_003078923
Ostreococcus lucimarinus / 1 / 2 / 0 / 0 / 1
XP_001419059 / XP_001419851
XP_001419478 / XP_001417318
Physcomitrella patens / 2 / 6 / 1 / 5 / 7
XP_001765894
XP_001766825 / XP_001771474
XP_001776547
XP_001772376
XP_001763232
XP_001768064
XP_001757752 / XP_001766838 / XP_001758774
XP_001757612
XP_001774238
XP_001785524
XP_001771484 / XP_001755215
XP_001769374
XP_001761737
XP_001758355
XP_001768791
XP_001772493
XP_001767359
Selaginella moellendorffii / 4 / 4 / 2 / 4 / 5
XP_002984293
XP_002966854
XP_002972463
XP_002961155 / XP_002967096
XP_002960915
XP_002976409
XP_002976336 / XP_002977037
XP_002964959 / XP_002987235
XP_002976402
XP_002976848
XP_002961712 / XP_002968717
XP_002988344
XP_002991584
XP_002960466
XP_002967256
Populus trichocarpa / 9 / 13 / 0 / 5 / 11
XP_002322093
XP_002331327
XP_002300882
XP_002314806
XP_002314421
XP_002312737
XP_002307544
XP_002317882
XP_002298926 / XP_002298015
XP_002320818
XP_002304516
XP_002298450
XP_002334994
XP_002323707
XP_002314017
XP_002302599
XP_002310398
XP_002310268
XP_002327783
XP_002306886
XP_002302017 / XP_002301806
XP_002303962
XP_002304373
XP_002323157
XP_002299172 / XP_002315388
XP_002310949
XP_002324775
XP_002326539
XP_002329737
XP_002330495
XP_002318307
XP_002311752
XP_002308276
XP_002335442
XP_002298538
Oryza sativa / 9 / 6 / 0 / 3 / 7
NP_001043794
NP_001056404
NP_001067677
NP_001043694
NP_001056342
NP_001043642
NP_001058530
NP_001057613
NP_001045815 / NP_001061028
NP_001065156
NP_001056846
NP_001049770
NP_001058471
NP_001045889 / NP_001056617
NP_001047841
NP_001051886 / NP_001057028
NP_001048341
NP_001049430
AAL58223
EEE65707
NP_001056806
NP_001043164
Arabidopsis thaliana / 8 / 12 / 0 / 3 / 10
MAPK8 AT1G18150
MAPK9 AT3G18040
MAPK15 AT1G73670
MAPK1 AT5G19010
MAPK17 AT2G01450
MAPK18 AT1G53510
MAPK19 AT3G14720
MAPK20 AT2G42880 / MAPK1 AT1G10210
MAPK2 AT1G59580
MAPK7 AT2G18170
MAPK14 AT4G36450
MAPK5 AT4G11330
MAPK11 AT1G01560
MAPK13 AT1G07880
MAPK12 AT2G46070
MAPK4 AT4G01370
MAPK6 AT2G43790
MAPK3 AT3G45640
MAPK10 AT3G59790 / MAPK21 AT4G13020
MAPK22 AT4g19110
MAPK23 AT5g45430 / MKK1 AT4G26070
MKK2 AT4G29810
MKK3 AT5G40440
MKK4 AT1G51660
MKK5 AT3G21220
MKK6 AT5G56580
MKK7 AT1G18350
MKK8 AT3G06230
MKK9 AT1G73500
MKK10 AT1G32320
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Table S2. Orthologs of Arabidopsis MAPKs and MKKs as suggested by ortholog identifier programsOrthologs of Arabidopsis MAPKs as determined by the InParanoid ortholog identifier program.
Arabidopsis thaliana / Selaginella moellendorffii / Physcomitrella patens / Chlamydomonas reinhardtii / Volvox carteri / Ostreococcus lucimarinus / Ostreococcus tauri / Micromonas sp. RCC299 / Naegleria gruberi
MAPK / TDY
Group D / MPK8 AT1G18150 / XP_001694300_chl / XP_002954367_vol / XP_001419059_olu / XP_003080614_ota / XP_002503335_mic
MPK9 AT3G18040 / XP_001694300_chl / XP_002954367_vol / XP_001419059_olu / XP_003080614_ota / XP_002503335_mic / XP_002672114_nag
MPK15 AT1G73670 / XP_001694300_chl / XP_002954367_vol / XP_001419059_olu / XP_003080614_ota / XP_002503335_mic
MPK16 AT5G19010 / XP_002961155_sel / XP_001694300_chl / XP_002954367_vol / XP_001419059_olu / XP_003080614_ota / XP_002503335_mic / XP_002672114_nag
XP_002966854_sel
MPK17 AT2G01450 / XP_001694300_chl / XP_002954367_vol / XP_001419059_olu / XP_003080614_ota / XP_002503335_mic
MPK18 AT1G53510 / XP_001694300_chl / XP_002954367_vol / XP_001419059_olu / XP_003080614_ota / XP_002503335_mic
MPK19 AT3G14720 / XP_001694300_chl / XP_002954367_vol / XP_001419059_olu / XP_003080614_ota / XP_002503335_mic / XP_002672114_nag
MPK20 AT2G42880 / XP_001765894_phy / XP_001694300_chl / XP_002954367_vol / XP_001419059_olu / XP_003080614_ota / XP_002503335_mic / XP_002672114_nag
XP_001766825_phy
TEY
Group C / MPK1 AT1G10210 / XP_002967096_sel / XP_001776547_phy / XP_002672114_nag
XP_002960915_sel / XP_001771474_phy
XP_002976409_sel
MPK2 AT1G59580 / XP_002967096_sel / XP_001776547_phy / XP_002672114_nag
XP_002960915_sel / XP_001771474_phy
XP_002976409_sel
MPK7 AT2G18170 / XP_002967096_sel / XP_001776547_phy / XP_002672114_nag
XP_002960915_sel / XP_001771474_phy
XP_002976409_sel
MPK14 AT4G36450 / XP_002967096_sel / XP_001776547_phy / XP_002672114_nag
XP_002960915_sel / XP_001771474_phy
XP_002976409_sel
Group B / MPK5 AT4G11330 / XP_002672114_nag
MPK11 AT1G01560
MPK13 AT1G07880 / XP_001700291_chl / XP_002955338_vol / XP_001419851_olu / XP_003081390_ota / XP_002503699_mic
MPK12 AT2G46070 / XP_002976336_sel / XP_001700291_chl / XP_002955338_vol / XP_001419851_olu / XP_003081390_ota / XP_002501054_mic
MPK4 AT4G01370 / XP_002976336_sel / XP_001763232_phy / XP_001700291_chl / XP_002955338_vol / XP_001419851_olu / XP_003081390_ota / XP_002501054_mic / XP_002672114_nag
Group A / MPK6 AT2G43790 / XP_001700291_chl / XP_002955338_vol / XP_001419851_olu / XP_003081390_ota / XP_002503699_mic / XP_002672114_nag
MPK3 AT3G45640 / XP_001700291_chl / XP_002955338_vol / XP_001419851_olu / XP_003081390_ota / XP_002501054_mic / XP_002672114_nag
MPK10 AT3G59790 / XP_001700291_chl / XP_001419851_olu / XP_003081390_ota / XP_002503699_mic / XP_002672114_nag
MHK / MPK21AT4G13020
MPK22 At4G19110 / XP_002987235_sel / XP_001757612_phy / XP_001697865_chl / XP_002949787_vol / XP_002505908_mic / XP_002675576_nag
XP_001785524_phy
XP_001774238_phy
MPK23 At5G45430 / XP_002987235_sel / XP_001757612_phy / XP_001697865_chl / XP_002949787_vol / XP_002505908_mic / XP_002675576_nag
XP_001785524_phy
XP_001774238_phy
Orthologs of Arabidopsis MAPKs as determined by the PLAZA plant comparative genomics platform
Arabidopsis thaliana / Selaginella moellendorffii / Physcomitrella patens / Chlamydomonas reinhardtii / Volvox carteri / Ostreococcus lucimarinus / Ostreococcus tauri / Micromonas sp. RCC299 / Naegleria gruberi
Group D / 8,9,15,16,17,18,19,20 / XP_002966854 / XP_001765894 / XP_001694300 / XP_002954367 / XP_001419059 / XP_003080614 / XP_002503335
XP_002984293 / XP_001766825
Group C / 1,2,7,14 / XP_002960915 / XP_001771474 / XP_001690850
Group B / 4,11,12 / XP_002976336 / XP_001763232 / XP_002503699
Group A / 6 / XP_001700291 / XP_002955338 / XP_001419851 / XP_003081390
3,5,10,13 no
ortholog
MHK / 21.22 / XP_002976402 / XP_001757612 / XP_001697865 / XP_002949787 / XP_002505908
XP_001774238
XP_001785524
23 no ortholog
Orthologs of Arabidopsis MKKs as determined by the PLAZA plant comparative genomics platform
Arabidopsis thaliana / Selaginella moellendorffii / Physcomitrella patens / Chlamydomonas reinhardtii / Volvox carteri / Ostreococcus lucimarinus / Ostreococcus tauri / Micromonas sp. RCC299 / Naegleria gruberi
Group A / MKK6 AT5G56580 / XP_002968717 / XP_001758355 / XP_001693665 / XP_002947566 / XP_002504085
XP_001761737
XP_001768791
Group B / MKK3 AT5G40440 / XP_002960466 / XP_001767359 / XP_001696437 / XP_002958286 / XP_002506404
XP_001772493
Group D / MKK9 AT1G73500 / XP_002991584 / XP_001755215
XP_001769374
1,2,4,5,7,8,10 no ortholog
Orthologs of Arabidopsis MKKs as determined by the InParanoid ortholog identifier program
Arabidopsis thaliana / Selaginella moellendorffii / Physcomitrella patens / Chlamydomonas reinhardtii / Volvox carteri / Ostreococcus lucimarinus / Ostreococcus tauri / Micromonas sp. RCC299 / Naegleria gruberi
Group A / MKK1 / XP_002947566_vol / XP_001417318_olu / XP_003078923_ota / XP_002504085_mic / XP_002675852_nag
MKK2 / XP_002947566_vol / XP_001417318_olu / XP_003078923_ota / XP_002504085_mic / XP_002675852_nag
MKK6 / XP_002988344_sel / XP_001758355_phy / XP_002947566_vol / XP_001417318_olu / XP_003078923_ota / XP_002504085_mic / XP_002675852_nag
XP_001768791_phy
Group B / MKK3 / XP_002960466_sel / XP_001767359_phy / XP_001696437_chl / XP_001417318_olu / XP_003078923_ota / XP_002675852_nag
XP_001772493_phy
Group C / MKK4
MKK5
Group D / MKK7 / XP_002991584_sel / XP_001769374_phy
XP_002968717_sel / XP_001755215_phy
MKK8 / XP_002991584_sel / XP_001769374_phy
XP_002968717_sel / XP_001755215_phy
MKK9 / XP_002991584_sel / XP_001769374_phy
XP_002968717_sel / XP_001755215_phy
MKK10
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Table S3. References for MKK–MPK interactions as depicted in Figure 3Yeast
Interaction / References (low throughput) / References (high throughput)
MKK1 -> SLT2 / PUBMED:9493378, PUBMED:8596433, PUBMED:17711850, PUBMED:8596433, PUBMED:22006927 / PUBMED:20489023, PUBMED:21118957
MKK2 -> SLT2 / PUBMED:11805837, PUBMED:8596433, PUBMED:17711850, PUBMED:8757399 / PUBMED:20489023, PUBMED:11805837
PBS2 -> HOG1 / PUBMED:9180081, PUBMED:18212044, PUBMED:21698101 / PUBMED:21118957
STE7 -> FUS3 / PUBMED:19303851, PUBMED:8668180, PUBMED:15456892, PUBMED:8384702 / PUBMED:20489023, PUBMED:21118957
STE7 -> HOG1 / PUBMED:20489023 / PUBMED:20489023
STE7 -> KSS1 / PUBMED: 19303851, PUBMED:11805837, PUBMED:8668180 / PUBMED:20489023
Human
Interactions / References (low throughput) / References (high throughput)
MEK1 -> MAPK1 / PUBMED:10757792 PUBMED:11134045 PUBMED:11226259 PUBMED:11266467 PUBMED:11279118 PUBMED:11352917 PUBMED:11741894 PUBMED:11823456 PUBMED:12697810 PUBMED:16887817 PUBMED:17255949 PUBMED:17367534 PUBMED:8670897
MEK1 -> MAPK3 / PUBMED:10748187 PUBMED:11134045 PUBMED:17367534 PUBMED:19197339 PUBMED:8226933 PUBMED:8626767 PUBMED:9006895 PUBMED:9733512
MEK2 -> MAPK1 / PUBMED:11823456
MEK2 -> MAPK3 / PUBMED:8626767 PUBMED:8226933 PUBMED:9006895
MEK3 -> MAPK14 / PUBMED:17255949 PUBMED:11279118
MEK3 -> MAPK3 / PUBMED:8226933
MEK4 -> MAPK8 / PUBMED:11823456 PUBMED:10713157 PUBMED:11279118
MEK4 -> MAPK9 / PUBMED:21900206
MEK5 -> MAPK7 / PUBMED:7759517
MEK6 -> MAPK14 / PUBMED:17255949 PUBMED:12697810 PUBMED:8622669 PUBMED:11279118
MEK7 -> MAPK8 / PUBMED:10713157 PUBMED:9207092
MEK7 -> MAPK14 / PUBMED:9207092
Arabidopsis
Interactions / References (low throughput) / References (high throughput)
MKK1 → MPK4 / PUBMED:18982020; PUBMED:9878570; PUBMED:9804171; PUBMED:19513235; PUBMED:15225555
MKK1 → MPK11 / PUBMED:19513235
MKK1 → MPK12 / PUBMED:19000167
MKK1 → MPK3 / PUBMED:17059410
MKK1 → MPK6 / PUBMED:17059410
MKK2 → MPK4 / PUBMED:18982020; PUBMED:9878570; PUBMED:19513235; PUBMED:15225555
MKK2 → MPK5 / PUBMED:15225555
MKK2 → MPK6 / PUBMED:19513235; PUBMED:15225555 / PUBMED:21798944
MKK2 → MPK10 / PUBMED:19513235
MKK2 → MPK11 / PUBMED:19513235
MKK2 → MPK13 / PUBMED:19513235
MKK3 → MPK1 / PUBMED:19513235
MKK3 → MPK2 / PUBMED:19513235
MKK3 → MPK7 / PUBMED:19513235
MKK3 → MPK14 / PUBMED:19513235
MKK3 → MPK6 / PUBMED:21419340
MKK3 → MPK8 / PUBMED:17369371
MKK4 → MPK3 / PUBMED:19513235 / PUBMED:21798944
MKK4 → MPK6 / PUBMED:19513235 / PUBMED:21798944
MKK5 → MPK3 / Doczi unpublished
MKK5 → MPK6 / PUBMED:19513235
MKK6 → MPK4 / PUBMED:21575092; PUBMED:20802223; PUBMED:19513235
MKK6 → MPK6 / PUBMED:21575092; PUBMED:19513235
MKK6 → MPK11 / PUBMED:21575092; PUBMED:19513235
MKK6 → MPK12 / PUBMED:20802223; PUBMED:19000167
MKK6 → MPK13 / PUBMED:21575092; PUBMED:20802223; PUBMED:19513235
MKK7 → MPK2 / PUBMED:19513235
MKK7 → MPK12 / PUBMED:19000167
MKK7 → MPK15 / PUBMED:19513235
MKK9 → MPK6 / PUBMED:19513235
MKK9 → MPK10 / PUBMED:19513235
MKK9 → MPK12 / PUBMED:19000167
MKK9 → MPK17 / PUBMED:19513235
MKK9 → MPK20 / PUBMED:19513235
MKK10 → MPK17 / PUBMED:19513235
Figure S1. Phylogenetic relationships of Ostreococcus, Micromonas, Volvox, Chlamydomonas, Physcomitrella, Selaginella, Arabidopsis and Naegleria MKKs and human MEK1. Lower plant MPK proteins were identified by using Arabidopsis query sequences in BLAST (http://blast.ncbi.nlm.nih.gov/) with individual organism sets. Retrieved sequences were filtered for the presence of the dual-specificity protein kinase catalytic domain consensus, the plant-specific MKK activation loop motif GTxxYMSPER and the plant-specific MKK phosphorylation site motif, [ST]xxxxx[ST]. Sequence alignment and phylogenetic analyses were conducted in the MEGA5 software suite (Tamura et al., Mol Biol Evol. 2011, 28:2731-9. PMID: 21546353). Protein kinase domains of each sequence were aligned by the MUSCLE alignment tool, using the following parameters: gap opening penalty: -2.9, gap extension penalty: -0.01, hydrophobicity multiplier: 1.2. The evolutionary history was inferred by using the Maximum Likelihood method based on the JTT matrix-based model. The bootstrap consensus tree inferred from 500 replicates is taken to represent the evolutionary history of the taxa analyzed. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (500 replicates) are shown next to the branches. Initial tree(s) for the heuristic search were obtained automatically as follows. When the number of common sites was < 100 or less than one fourth of the total number of sites, the maximum parsimony method was used; otherwise BIONJ method with MCL distance matrix was used. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. All positions containing gaps and missing data were eliminated. Proteins are designated by accession numbers (AGI numbers in case of Arabidopsis). Sequences are shown on a background coloured according to species for visual clarity. Species are indicated by the following abbreviations: ota: Ostreococcus tauri, olu: Ostreococcus lucimarinus, mic: Micromonas sp. RCC299, vol: Volvox carteri, chl: Chlamydomonas reinhardtii, phy: Physcomitrella patens, sel: Selaginella moellendorffii. Human MEK1 is indicated with the species acronym Hs. A, B, C, D and intermediate indicate A, B, C, D and ‘intermediate’ phylogenetic groups.
Figure S2. Phylogenetic relationships of Ostreococcus, Micromonas, Volvox, Chlamydomonas, Physcomitrella, Selaginella, Arabidopsis and Naegleria MAPKs and human MAPKs, representing major types of human MAPKs. Lower plant MPK proteins were identified by using Arabidopsis query sequences in BLAST (http://blast.ncbi.nlm.nih.gov/) with individual organism sets. Retrieved sequences were filtered for the presence of the serine/threonine kinase catalytic domain consensus, the plant-specific MAPK activation loop motifs (FMTEYVVTRWYRAPEL in case of TEY-type MAPKs, FWTDYVATRWYRAPEL in case of TDY-type MAPKs and PYT[ED]YVSTRWYRAPE in case of MHK-type kinases) including the MAPK phosphorylation site motif TxY. Sequence alignment and phylogenetic analyses were conducted in MEGA5 software suite (Tamura et al., Mol Biol Evol. 2011, 28:2731-9. PMID: 21546353). Protein kinase domains of each sequence were aligned by the MUSCLE alignment tool, using the following parameters: gap opening penalty: -2.9, gap extension penalty: -0.01, hydrophobicity multiplier: 1.2. The evolutionary history was inferred by using the Maximum Likelihood method based on the JTT matrix-based model. The bootstrap consensus tree inferred from 500 replicates is taken to represent the evolutionary history of the taxa analyzed. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (500 replicates) are shown next to the branches. Initial tree(s) for the heuristic search were obtained automatically as follows. When the number of common sites was < 100 or less than one fourth of the total number of sites, the maximum parsimony method was used; otherwise BIONJ method with MCL distance matrix was used. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. All positions containing gaps and missing data were eliminated. Proteins are designated by accession numbers (AGI numbers in case of Arabidopsis). Sequences are shown on a background coloured according to species for visual clarity. Species are indicated by the following abbreviations: ota: Ostreococcus tauri, olu: Ostreococcus lucimarinus, mic: Micromonas sp. RCC299, vol: Volvox carteri, chl: Chlamydomonas reinhardtii, phy: Physcomitrella patens, sel: Selaginella moellendorffii. Human MAPKs are indicated with the species acronym Hs. A, B, A/B, C, D and ERK8-like indicate A, B, A/B, C, D and ERK8-like phylogenetic groups.
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