Supplementary Material Bona fide choline monoxygenases evolved in Amaranthaceae plants from oxygenases of unknown function: evidence from phylogenetics, homology modeling and docking studies Javier Carrillo-Campos1, Héctor Riveros-Rosas2, Rogelio RodríguezSotres1, and Rosario A. Muñoz-Clares1* 1
Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México, 04510. México. 2
Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Ciudad de México, 04510. México.
*Correspondence: Rosario A. Muñoz-Clares, Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México, 04510. México. *E-mail:
[email protected] Tel: +52 5556223718 Short title: Evolution of choline monooxygenase proteins
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Supplementary Table S1. Proteins identified as members of the CMO subfamily Amino acid sequences were retrieved from NCBI or from Phytozome 12.1.5. * Sequences corrected by us; in these cases, the number of residues given in the table corresponds to the corrected sequence. ** The two domains of this protein are reported as separate sequences in the NCBI database, each with different accession number. SPECIES
Nannochloropsis gaditana Bathycoccus prasinos Coccomyxa subellipsoidea C-169 Chlorella variabilis Micromonas pusilla CCMP1545 Micromonas sp. RCC299 Monoraphidium neglectum Klebsormidium flaccidum Physcomitrella patens subsp. patens Sphagnum fallax Marchantia polymorpha Selaginella moellendorffii
ACCESSION NUMBER NCBI PHYTOZOME HETEROKONTHOPHYTA EWM23896 ⸺ CHLOROPHYTA XP_007511423 XP_005644270 XP_005645368 XP_005845791 XP_003061830 XP_002508933 XP_013903967 CHAROPHYTA GAQ84770 BRIOPHYTA XP_001752587
LENGTH
511 aa
⸺ ⸺ ⸺ ⸺ ⸺
452 aa* 368 aa 357 aa
⸺ ⸺
364 aa 448 aa
⸺
481 aa
Pp3c13_13580
414 aa
⸺ Sphfalx0064s0059 MARCHANTIOPHYTA OAE24413 Mapoly0089s0013 LYCOPODIOPHYTA XP_002981049 SELMODRAFT_114039 MONOCOTYLEDONS
434 aa* 338 aa
430 aa 441 aa* 410 aa 342 aa
OAY65202
⸺ evm_27.model.AmTr_v1.0_sca ffold00019.418 Aco012177LG02
Anthurium amnicola Brachypodium distachyon Brachypodium stacei Dichanthelium oligosanthes Elaeis guineensis Hordeum vulgare subsp. vulgare
JAT51600 XP_003563491 ⸺ OEL37452 XP_010927268 BAG74777
⸺ Bradi1g33960 Brast07G193900 ⸺ ⸺ ⸺
380 aa 409 aa 408 aa
Leymus chinensis Musa acuminata Ophiopogon japonicus Oropetium thomaeum Oryza brachyantha Oryza sativa Japonica Group
ABV64740 XP_009410214 ABG34274 ⸺ XP_006657294 XP_015643170
⸺ GSMUA_Achr7T19580_0 Oropetium_20150105_16264 ⸺ ⸺
342 aa 425 aa 438 aa 308 aa 362 aa 410 aa
EEC81252
LOC_Os06g48510
410 aa
Aegilops tauschii Amborella trichopoda Ananas comosus
Oryza sativa Indica Group
EMT07994 XP_006845775
422 aa 420 aa
414 aa* 426 aa 407 aa
2
SPECIES Panicum halli
NCBI ⸺
ACCESSION NUMBER PHYTOZOME Pahal.D00004
LENGTH 407 aa
Phoenix dactylifera Setaria italica
⸺ ⸺ XP_008801514 XP_004966128
Pavir.J39646 Pavir.Db00260 ⸺ Si006556m.g
363 aa* 316 aa* 426 aa 411 aa
Setaria viridis Sorghum bicolor Spirodela polyrrhiza Triticum aestivum Triticum monococcum subsp. aegilopoides
⸺ XP_002437525 ⸺ AMA02065 AKZ66518
Sevir.4G257300 Sb10g028700 Spipo5G0003400 ⸺ ⸺
411 aa 405 aa 322 aa 411 aa* 86 aa
EMS46986 NP_001105926 KMZ72255 EUDICOTYLEDONS
⸺ Zm00008a024486 ZOSMA_169G00470
365 aa* 408 aa 413 aa
⸺
AHYPO_002206-RA AHYPO_004856-RA
439 aa 421 aa
Arabidopsis halleri Arabidopsis lyrata subsp. lyrata
BAF93187 ⸺ KFK29548 KFK40841 ⸺ XP_002869406
⸺ Aqcoe7G261800 ⸺ ⸺ Araha.6052s000 AL7G22360
442 aa 428 aa 420 aa 236 aa 423 aa 422aa
Arabidopsis thaliana Arachis duranensis Arachis ipaensis Atriplex amnicola Atriplex canescens Atriplex hortensis
NP_194718 XP_015973237 XP_016201893 AHH24260 AFG28558 Q9LKN0
At4g29890 ⸺ ⸺ ⸺ ⸺ ⸺
422 aa 418 aa 418 aa 438 aa 438 aa 438 aa
Atriplex nummularia Atriplex prostrata Atriplex semibaccata Bassia scoparia
BAC77698 AAL9256 AGC13074 AAQ92313 XP_010682183 XP_010667950
⸺ ⸺ ⸺ ⸺ ⸺ ⸺
438 aa 438 aa 438 aa 290 aa 446 aa 418 aa
⸺ XP_013738248 XP_013705395 XP_013596413 XP_009137872 KYP52554
Bostr.7867s083 ⸺ ⸺ Bol033622 Brara.K00866 ⸺
424 aa 440 aa 438 aa 438 aa 432 aa 416 aa
AFP19450
⸺
434 aa
Panicum virgatum
Triticum urartu Zea mays Zostera marina
Amaranthus hypochondriacus Amaranthus tricolor Aquilegia coerulea Arabis alpina
Beta vulgaris Boechera stricta Brassica napus Brassica oleraceae Brassica rapa Cajanus cajan Camellia sinensis
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Capsella rubella Capsella grandiflora
ACCESSION NUMBER NCBI PHYTOZOME XP_010433050 ⸺ XP_010436340 ⸺ XP_010438247 ⸺ XP_010447794 ⸺ XP_006285614 Carubv10007064m.g ⸺ Cagra.0268s0015
Capsicum annuum Cephalotus follicularis Chrysanthemum lavandulifolium Cicer arietinum Citrus clementina Citrus sinensis
XP_016556147 GAV59711 ABX57826 XP_004507911 XP_006453220 XP_006474292
⸺ ⸺ ⸺ ⸺ Ciclev10008481m.p ⸺
422 aa 418 aa 201 aa 414 aa 408 aa 413 aa
Coffea canephora
⸺
431 aa
⸺
395 aa
Corchorus olitorius Cynara cardunculus Cucumis melo Cucumis sativus Daucus carota Dorcoceras hygrometricum
CDP08949 OMP06320OMO52515** OMO51681 KVI11819 XP_008443631 XP_004139149 XP_017254907 KZV50441
⸺ ⸺ ⸺ Cucsa.356080 DCAR_020143 ⸺
364 aa 411 aa* 417 aa 417 aa 415 aa
Eucalyptus camaldulensis Eucalyptus grandis Eutrema salsugineum Fragaria vesca subsp. vesca Glycine max Gossypium arboreum
ABS71853 XP_010046909 XP_006412796 XP_004301419 XP_003549280 XP_017612508
⸺ EUGRSUZ_C00087 Thhalv10025251m mrna12324.1-v1.0 Glyma.17G057700 ⸺
429 aa* 429 aa 432 aa 410 aa 418 aa 444 aa
Gossypium raimondii Haloxylon ammodendron Haloxylon persicum Ipomoea nil
XP_016719040 XP_016686114 XP_012459381 ACX47904 AEW31326 XP_019182381
⸺ ⸺ Gorai.012G008200 ⸺ ⸺ ⸺
381 aa 409 aa 428 aa 448 aa 447 aa 418 aa
Jatropha curcas Juglans regia Kalanchoe fedtschenkoi
XP_012074438 XP_018807260 ⸺
⸺ ⸺ Kaladp0809s0111 Kalax.0333s0026 Kalax.0012s0114 Lus10032689
414 aa 430 aa 462 aa 462 aa 462 aa 427 aa
Lus10008571 ⸺
427 aa 427 aa
SPECIES
Camelina sativa
Corchorus capsularis
Gossypium hirsutum
Kalanchoe laxiflora
⸺
Linum usitatissimum
⸺
Lycium barbarum
ACR15118
LENGTH 427 aa 286 aa 427 aa 427 aa 423 aa 423 aa
416 aa*
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SPECIES Lupinus angustifolius Malus domestica Manihot esculenta Medicago truncatula Mimulus guttatus Morus notabilis Nelumbo nucifera Nicotiana attenuata Nicotiana sylvestris Nicotiana tabacum Nicotiana tomentosiformis Phaseolus vulgaris Populus euphratica Populus trichocarpa Prunus persica Prunus mume Pyrus betulifolia Pyrus bretschneideri Raphanus sativus Ricinus communis Salicornia bigelovii Salicornia europaea Salix purpurea Sesamum indicum Solanum lycopersicum Solanum penelli Solanum tuberosum Spinacia oleracea Suaeda liaotungensis Suaeda maritima Suaeda salsa Tarenaya hassleriana
ACCESSION NUMBER NCBI PHYTOZOME XP_019463425 ⸺
LENGTH 411 aa
XP_008391562 XP_008351406 OAY46667 XP_003610028 XP_012828802 EYU18199
MDP000022353 MDP000031939 Manes.06G017600 MTR_4g127130 MIMGU_mgv1a006513mg MIMGU_mgv1a006978mg
405 aa 359 aa 417 aa 411 aa 433 aa 424 aa
XP_010094241 XP_010276721 OIT26339 XP_009757252 XP_016508540 XP_016460838
⸺ ⸺ ⸺ ⸺ ⸺ ⸺
407 aa* 420 aa 480 aa 427 aa 436 aa 427 aa
XP_009601434 XP_007154695 XP_00713286 XP_00713485 XP_011020077 XP_002308100
⸺ Phvul.003G140100 Phvul.011G131100 Phvul.010G082000 ⸺ POPTR_0006s07230
436 aa 416 aa 200 aa 188 aa 424 aa 424 aa
ONI27175 XP_008223853 AER10510 XP_009343851 XP_018435688 XP_018481725
Prupe.1G072500 ⸺ ⸺ ⸺ ⸺ ⸺
414 aa 414 aa 405 aa 405 aa 457 aa 456 aa
XP_002518256 AJF98574 AAV91779 ⸺ XP_011094129 XP_004242785
30198.t000028 ⸺ ⸺ SapurV1A.0198s0060 ⸺ Solyc07g008310
417 aa 439 aa 442 aa 424 aa 435 aa 412 aa
XP_004243034 XP_015080536 XP_015081828 NP_001275051 XP_021849509 XP_021866412
Solyc07g009300 ⸺ ⸺ PGSC0003DMT400051201 ⸺ ⸺
410 aa 412 aa 410 aa 412 aa 439 aa 426 aa
AAM43920 AFW04225 ABG43004 XP_010541096
⸺ ⸺ ⸺ ⸺
442 aa 442 aa 442 aa 438 aa
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SPECIES Theobroma cacao Trifolium pratense Trifolium subterraneum Vigna angularis Vigna radiata Vitis vinifera Ziziphus jujuba
Branchiostoma belcheri
Branchiostoma floridae
Saccoglossus kowalevskii
Acanthamoeba castellanii
ACCESSION NUMBER NCBI PHYTOZOME EOY05290 Thecc1EG020326t1 Tp57577_TGAC_v2_mRNA55 ⸺ 77 GAU38011 ⸺
LENGTH 407 aa 432 aa 390 aa
XP_017410379 XP_014508581 XP_019078540 XP_015889685 CHORDATA XP_019633636
⸺ ⸺ GSVIVT01029282001 ⸺
416 aa 416 aa 441 aa 404 aa
⸺
418 aa
XP_019618440 XP_019644608 XP_019644788 XP_002599795 XP_002597329 XP_002610312
⸺ ⸺ ⸺
409 aa 449 aa 442 aa 381 aa 410 aa 357 aa
HEMICHORDATA XP_002738379 XP_006820984 XP_002737044 AMOEBOZOA XP_004333794
400 aa 403 aa 416 aa ⸺
458 aa
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