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SI CHI Evolution

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SI CHI Evolution Supporting Information for Kaltenbach at al., Evolution of chalcone isomerase from a non-catalytic ancestor Table of Contents Table S1. Protein sequences used for the structure-based alignment (Figure S1, Supplementary Data Set 1). p. 1 Figure S1. Structure-based alignment of representative ancestral and extant sequences used in this work. p. 3 Figure S2. Phylogenetic tree used for the ancestral reconstruction. p. 4 Figure S3. An advanced guide to ancestral sequence inference with no headaches (or fewer, at least): representative example of the decision-making process to determine the amino acid sequence in ambiguously inferred positions. p. 8 Table S2. Posterior probabilities of the initial ancestral reconstruction including indels and final amino acid sequences of the ancestral proteins after manual revision of ambiguously inferred positions in gap regions (Figure S3) and at the termini (Figure S1). p. 9 Table S3. Apparent midpoint denaturation temperatures (Tm) of selected variants measured using SYPRO Orange as fluorescent probe and/or by NanoDSF (following Tryptophane fluorescence). p. 16 Figure S4. Correlation between Tm values determined using SYPRO Orange and NanoDSF. p. 16 Table S4. Enzymatic activities of CHI from A. thaliana (AtCHI), inferred ancestors and variants obtained by directed evolution. p. 17 Figure S5. Spontaneous isomerization of chalconaringenin to racemic naringenin. p. 18 Figure S6. Analysis of the evolutionary conservation and position of residues to generate ancCHI*. p. 19 Table S5. Mutagenic primers used for phylogenetic library generation. p. 20 Table S6. Overview of library generation and screening throughput. p. 21 Table S7. Sequenced variants of the phylogenetic libraries. p. 21 Table S8. Mutations accummulated in the phylogenetic trajectory. p. 29 Table S9. Enzymatic activities of variants obtained by additional library screening or site-directed mutagenesis. p. 29 Table S10. Sequenced variants of the low-mutation rate phylogenetic libraries. p. 30 Table S11. Sequenced variants of the random mutagenesis libraries. p. 33 Table S12. Occurrence of phylogenetic founder mutations and epR4 mutations in the ancestral reconstruction and in extant sequences. p. 35 Table S13. Mutations accummulated in the alternative random mutagenesis trajectory. p. 35 Table S14. Data collection and refinement statistics for x-ray protein structures determined in this work. p. 36 Figure S7. X-ray crystal structures reported in this work. p. 37 Table S15. RMS values for protein-protein structural alignments based on CA alignments in PyMOL. p. 39 Figure S8. Average distance of each mutation from ancR1, ancR2, ancR3, ancR5, and ancR7 calculated as the distance from the side chain Cβ to Nε of R34. p. 40 Figure S9. Root mean square deviations (RMSD, Å) of all substrate heavy atoms from simulations of ancCC, ancR1, ancR3, ancR7, ancCHI and AtCHI Michaelis complexes. p. 41 Figure S10. Overview of simulations of the ancCHI and AtCHI Michaelis complexes, showing the distribution of different substrate binding modes in each simulation. p. 42 Figure S11. Illustration of different substrate binding modes observed in our molecular dynamics simulations using the ancR3 variant as a representative example. p. 43 Figure S12. Root-mean square deviations (RMSD) of all product heavy atoms from simulations of ancCC and ancR1 in complex with the product observed in the non- productive binding mode. p. 44 Figure S13. NMR 15N-1H HSQC spectra of ancCC (blue), ancR1 (red), and ancR7 (purple). p. 45 Figure S14. Root-mean square fluctuations (RMSF) of Arg34 during our substrate- free simulations of the ancCC, ancR1, ancR3 and ancR7 variants. p. 46 Figure S15. Root-mean square deviations (RMSD, Å) of all backbone heavy atoms from simulations of the different enzymes. p. 47 Table S16. Standard GAFF atom types and calculated partial charges used to describe the substrate chalconaringenin (left) and the product naringenin (right) p. 48 References p. 49 2 Table S1. Protein sequences used for the structure-based alignment (Figure S1, Supplementary Data Set 1). Protein Family Major Clade Clade Family Species Sequence Identifier[a] CHI Angiosperms Basal Eudicots Proteaceae Grevillea robusta GRRW-56937 CHI Angiosperms Basal Eudicots Papaveraceae Eschscholzia californica RKGT-57420 CHI Angiosperms Basalmost angiosperms Austrobaileyaceae Austrobaileya scandens FZJL-165039 CHI Angiosperms Basalmost angiosperms Ceratophyllaceae Ceratophyllum demersum NPND-121635 CHI Angiosperms Basalmost angiosperms Nymphaeaceae Nymphaea sp. PZRT-6817 CHI Angiosperms Basalmost angiosperms Amborellaceae Amborella trichopoda URDJ-33860 CHI Angiosperms Chloranthales Chloranthaceae Sarcandra glabra OSHQ-47092 CHI Angiosperms Core Eudicots Santalaceae Daenikera sp. BSEY-12135 CHI Angiosperms Core Eudicots Basellaceae Basella alba CTYH-26097 CHI Angiosperms Core Eudicots Crassulaceae Kalanchoe crenato-diagremontiana DRIL-14508 CHI Angiosperms Core Eudicots Nyctaginaceae Allionia incarnata EGOS-1705 CHI Angiosperms Core Eudicots Nyctaginaceae Allionia incarnata HMFE-18529[b] CHI Angiosperms Core Eudicots Molluginaceae Mollugo pentaphylla KJAA-23136[c] CHI Angiosperms Core Eudicots Physenaceae Physena madagascariensis RUUB-84668 CHI Angiosperms Core Eudicots Phytolaccaceae Hilleria latifolia SFKQ-89198 CHI Angiosperms Core Eudicots Molluginaceae Mollugo nudicaulis UNSW-124362 CHI Angiosperms Core Eudicots Ranunculaceae Aquilegia formosa CHI_Afor CHI Angiosperms Core Eudicots/Asterids Gentianaceae Gentriana triflora CHI_Gtri CHI Angiosperms Core Eudicots/Asterids Solanaceae Nicotiana tobacum CHI_Ntab CHI Angiosperms Core Eudicots/Asterids Asteraceae Tanacetum parthenium DUQG-51806 CHI Angiosperms Core Eudicots/Asterids Stylidiaceae Stylidium adnatum FXGI-5812 CHI Angiosperms Core Eudicots/Asterids Goodeniaceae Scaevola mossambicensis HUQC-70359 CHI Angiosperms Core Eudicots/Asterids Oleaceae Chionanthus retusus KTAR-140005 CHI Angiosperms Core Eudicots/Asterids Montiniaceae Kaliphora madagascariensis KTWL-19787 CHI Angiosperms Core Eudicots/Asterids Asteraceae Matricaria matricarioides OAGK-54163 CHI Angiosperms Core Eudicots/Asterids Asteraceae Matricaria matricarioides OAGK-55018 CHI Angiosperms Core Eudicots/Asterids Asteraceae Flaveria trinervia ZCUA-8524[d] CHI Angiosperms Core Eudicots/Asterids Asteraceae Lactuca graminifolia ZGDS-88797 CHI Angiosperms Core Eudicots/Asterids Convolvulaceae Ipomoea batatas CHI_Ibat CHI Angiosperms Core Eudicots/Rosids Brassicaceae Arabidopsis thaliana CHI_Atha CHI Angiosperms Core Eudicots/Rosids Elaeagnaceae Elaeagnus umbellata CHI_Eumb CHI Angiosperms Core Eudicots/Rosids Fabaceae Medicago sativa CHI_Msat CHI Angiosperms Core Eudicots/Rosids Bataceae Batis maritima DZTK-39299 CHI Angiosperms Core Eudicots/Rosids Rhamnaceae Rhamnus japonica EILE-39733 CHI Angiosperms Core Eudicots/Rosids Rhamnaceae Rhamnus japonica EILE-6281 CHI Angiosperms Core Eudicots/Rosids Fabaceae Astragalus membranaceus HJMP-10325 CHI Angiosperms Core Eudicots/Rosids Linaceae Linum hirsutum HNCF-62563 CHI Angiosperms Core Eudicots/Rosids Myrtaceae Syzygium micranthum NEBM-18344 CHI Angiosperms Core Eudicots/Rosids Coriariaceae Coriaria nepalensis NNGU-23905 CHI Angiosperms Core Eudicots/Rosids Quillajaceae Quillaja saponaria OQHZ-20024 CHI Angiosperms Core Eudicots/Rosids Passifloraceae Passiflora caerulea SIZE-3368 CHI Angiosperms Core Eudicots/Rosids Onagraceae Oenothera serrulata SJAN-10048 CHI Angiosperms Core Eudicots/Rosids Euphorbiaceae Euphorbia mesembryanthemifolia VPDX-44653 CHI Angiosperms Core Eudicots/Rosids Rhamnaceae Rhamnus caroliniana WVEF-12235 CHI Angiosperms Core Eudicots/Rosids Lythraceae Punica granatum YNUE-90967[e] CHI Angiosperms Core Eudicots/Rosids Anacardiaceae Rhus radicans YUOM-36840 CHI Angiosperms Core Eudicots/Rosids Krameriaceae Krameria lanceolata ZHMB-85808 CHI Angiosperms Magnoliids Piperaceae Piper auritum MUNP-769 CHI Angiosperms Magnoliids Myristicaceae Myristica fragrans OBPL-45593 CHI Angiosperms Magnoliids Aristolochiaceae Aristolochia elegans PAWA-45302 CHI Angiosperms Magnoliids Winteraceae Drimys winteri WKSU-130380 CHI Angiosperms Monocots Hemerocallidaceae Hemerocallis spp. BLAJ-12405 CHI Angiosperms Monocots Amaryllidaceae Allium cepa CHI_Acep CHI Angiosperms Monocots Pandanaceae Freycinetia multiflora DGXS-9913 CHI Angiosperms Monocots Amaryllidaceae Rhodophiala pratensis JDTY-16234 CHI Angiosperms Monocots Asphodelaceae Aloe vera JVBR-9654 CHI Angiosperms Monocots Velloziaceae Talbotia elegans SILJ-81872 CHI Angiosperms Monocots Orchidaceae Vanilla planifolia THDM-62163 CHI Angiosperms Monocots Xanthorrhoeaceae Johnsonia pubescens WTDE-8108 CHI Angiosperms Monocots/Commelinids Cannaceae Canna x generalis CHI_Cgen CHI Angiosperms Monocots/Commelinids Arecaceae Elaeis oleifera CHI_Eole CHI Angiosperms Monocots/Commelinids Poaceae Oryza sativa CHI_Osat CHI Angiosperms Monocots/Commelinids Cyperaceae Mapania palustris XPAF-10253 CHI Angiosperms Monocots/Commelinids Arecaceae Typhonium blumei YMES-18290 CHI Ferns Eusporangiate Monilophytes Ophioglossaceae Sceptridium dissectum EEAQ-85524 CHI Ferns Eusporangiate Monilophytes Equisetaceae Equisetum hyemale JVSZ-131011 CHI Ferns Eusporangiate Monilophytes Marattiaceae Angiopteris evecta NHCM-64613 CHI Ferns Leptosporangiate Monilophytes Anemiaceae Anemia tomentosa CQPW-971 CHI Ferns Leptosporangiate Monilophytes Pteridaceae Argyrochosma nivea XDDT-6681 CHI Gymnosperms Conifers Cupressaceae Tetraclinis sp. CGDN-7669 CHI Gymnosperms Conifers Pinaceae Pinus jeffreyi CHI_Pjef
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