Volume 7, Issue 1, Pages 101-120 (January 2014) High-Resolution Crystal Structure and Redox Properties of Chloroplastic Triosephosphate Isomerase from Chlamydomonas reinhardtii  Mirko Zaffagnini, Laure Michelet, Chiara Sciabolini, Nastasia Di Giacinto, Samuel Morisse, Christophe H. Marchand, Paolo Trost, Simona Fermani, Stéphane D Lemaire  Molecular Plant  Volume 7, Issue 1, Pages 101-120 (January 2014) DOI: 10.1093/mp/sst139 Copyright © 2013 The Authors. All rights reserved. Terms and Conditions

Figure 1 Multiple Sequence Alignment of TPIs from Diverse Organisms and Secondary Structure Elements of CrTPI. Residues of CrTPI are numbered according to the mature sequence. Abbreviations and accession numbers: TPI_CHLRE, Chlamydomonas reinhardtii TPI, Q5S7Y5; chTPI_ARATH, Arabidopsis thaliana chloroplastic TPI, Q9SKP6.1; cyTPI_ARATH, Arabidopsis thaliana cytoplasmic TPI, P48491.2; TPI_RABIT, Oryctolagus cuniculus TPI, P00939.1; TPI_HUMAN, Homo sapiens TPI, P60174.1; TPI_PLAFA, Plasmodium falciparum TPI, Q07412.1; TPI_GIAIN, Giardia Lamblia TPI, P36186.1; TPI_TRYBB, Trypanosoma brucei TPI, P04789.2. Conserved residues are marked by an asterisk (*). The catalytic residues (Asn11, Lys13, His95, and Glu167) are highlighted in blue. The cysteine residues are highlighted in green. Secondary structures are indicated as follows: yellow arrows for β-strands, red and orange cylinders for α-helix and the 310 helices, respectively, and green lines for loops. The sequences were aligned with the ClustalW2 program (www.ebi.ac.uk/Tools/msa/clustalw2/). Molecular Plant 2014 7, 101-120DOI: (10.1093/mp/sst139) Copyright © 2013 The Authors. All rights reserved. Terms and Conditions

Figure 2 Kinetic Analysis of CrTPI. (A) Linear dependence of TPI activity on protein concentration expressed as ΔAbs340 min−1. The data are represented as mean ± SD (n = 3). (B) Variations of apparent velocity (V) catalyzed by 0.78nM CrTPI in the presence of varying G3P concentrations. Turnover represents moles of NADH oxidized s−1 by 1 mol of CrTPI. Michaelis–Menten and Lineweaver–Burk (inset) plots of V versus (G3P) are shown. Data are represented as mean ± SD (n = 3). The kinetic parameters were calculated using only non-linear curve fit of the data sets. Molecular Plant 2014 7, 101-120DOI: (10.1093/mp/sst139) Copyright © 2013 The Authors. All rights reserved. Terms and Conditions

Figure 3 Dimeric and Monomeric Fold of CrTPI. (A) Cartoon representation of the CrTPI homodimer. The crystallographic independent subunit A is colored accordingly to the secondary structure elements and the β-strands are numbered accordingly to the TIM-barrel fold. The second subunit (A′) is formed by a two-fold crystallographic axis, indicated by a black line and coincident with the molecular axis. (B) Different views, rotated by 90º, of the CrTPI monomer showing the characteristic TIM-barrel fold. Both panels were prepared by Pymol software (The PyMOL Molecular Graphics System, Version 1.5.0.4 Schrödinger, LLC). Molecular Plant 2014 7, 101-120DOI: (10.1093/mp/sst139) Copyright © 2013 The Authors. All rights reserved. Terms and Conditions

Figure 4 Superimposition of TPI Monomers. (A) Superimposition of CrTPI polymorph 1 (green), polymorph 3 subunit E (yellow), OcTPI subunit A (light blue), and OcTPI subunit B (blue) structures. The loop 6 and the adjacent loops 5 and 7 are indicated. (B) Zoom on the loop-6 region showing the ‘open’ and ‘closed’ conformations observed in subunits A and B of OcTPI, respectively. The conformation of the loop 6 of CrTPI polymorph 1 is similar to OcTPI subunit A, while the loop 6 of polymorph 3 subunit E shows a more open conformation. Both panels were prepared by Pymol software (The PyMOL Molecular Graphics System, Version 1.5.0.4 Schrödinger, LLC). Molecular Plant 2014 7, 101-120DOI: (10.1093/mp/sst139) Copyright © 2013 The Authors. All rights reserved. Terms and Conditions

Figure 5 Catalytic Site and Position of Cysteine Residues in CrTPI Dimer. (A) Cartoon representation of the CrTPI homodimer indicating the position of the active site in subunit A colored in green. The catalytic residues Asn11, Lys13, His95, and Glu167 all belonging to the same subunit, other conserved residues contributing to the active site as Ser96, Glu97, and Cys126 and a MPD molecule are shown in sticks. Water molecules are shown as red spheres. Loop-3 and Thr75, belonging to the other subunit (indicated as A′) and participating to the active site formation, are shown in magenta. The position of the five cysteine residues, shown as sticks, and catalytic loop 6 is indicated by labels. (B) Zoom on the active site illustrating the H-bond network among side chain residues forming the catalytic site, water molecules contained in the cavity, and a MPD molecule located on top of the active pocket. The catalytic Glu167 in ‘swung in’ conformation and the G3P molecule in complex with TbTPI (PDB code 6TIM) are represented by light-gray sticks. The figure was prepared by Pymol software (The PyMOL Molecular Graphics System, Version 1.5.0.4 Schrödinger, LLC). Molecular Plant 2014 7, 101-120DOI: (10.1093/mp/sst139) Copyright © 2013 The Authors. All rights reserved. Terms and Conditions

Figure 6 Short- and Long-Range Interactions and Molecular Environment of CrTPI Cysteines. Short-range (<4 Å) and long-range (<15 Å) distance interactions shown by dashed lines, with basic and acid residues of thiol group of (A) Cys14 (long-range distances: Cys14(A)SG–Lys13(A)NZ 11.04 Å; –Glu77(A′)OE1 6.93 Å; –Glu181(A′)OE1 7.23 Å); (B) Cys126 (long-range distances Cys126(A)SG–His95(A)NE2 5.57 Å; –Arg99(A)NH2 7.46 Å; –Glu167(A)OE1 4.12 Å); (C) Cys194 (long-range distances Cys194(A)SG–Arg191(A)NH1 7.02 Å; –Lys197(A)NZ 9.97 Å; –Lys196(A)NZ 10.98 Å; –Asp144(A)OD1 9.50 Å; –Asp148(A)OD1 9.50 Å); (D) Cys247 (long-range distances Cys247(A)SG–Lys253(A)NZ 14.66 Å); (E) Cys219 (long-range distances Cys219(A)SG–Lys220(A)NZ 6.60 Å; –Lys224(A)NZ 11.55 Å; –Asp216(A)OD1 7.29 Å; –Asp221(A)OD2 8.38 Å). The residues are shown in sticks, the green color is used for residues of subunit A, while magenta is used for residues belonging to the other subunit A′. (F) Molecular environment of Cys219 shown as surface representation. The basic and acidic residues surrounding the cysteine are indicated with labels—blue: basic amino groups; red: acidic groups; and yellow: thiol groups. All panels were prepared by Pymol software (The PyMOL Molecular Graphics System, Version 1.5.0.4 Schrödinger, LLC). Molecular Plant 2014 7, 101-120DOI: (10.1093/mp/sst139) Copyright © 2013 The Authors. All rights reserved. Terms and Conditions

Figure 7 Reaction of DTNB with CrTPI. (A) Quantification of cysteine thiols in CrTPI monomer. The number of free cysteine thiols was determined by measuring TNB− formation at 412nm during incubation of CrTPI with DTNB. Data represent the average (± SD) of three independent experiments. (B) Effect of DTNB on CrTPI activity. Reduced protein was incubated for 30min in the presence of DTNB in a 10-fold DTNB:protein molar ratio. At indicated times, an aliquot was withdrawn to assess residual activity. (C) Reversibility of DTNB-dependent inhibition of CrTPI. The reactivation of CrTPI after 10-min incubation with DTNB was assessed by measuring TPI activity after 15-min incubation in the presence of 20mM DTT. For panels (B) and (C), data are represented as mean percentage ± SD (n = 3) of initial activity of reduced CrTPI. Molecular Plant 2014 7, 101-120DOI: (10.1093/mp/sst139) Copyright © 2013 The Authors. All rights reserved. Terms and Conditions

Figure 8 Effects of H2O2 and GSSG on CrTPI and CrICL Activities. (A) Incubation of CrTPI and CrICL in the presence of H2O2. Reduced proteins (left side, CrTPI; right side, CrICL) were incubated for 30min in the presence of 0.1mM H2O2 (black bars). The reversibility of CrTPI and CrICL inactivation was assessed by incubation in the presence of 20mM DTT (white bars). Data are represented as mean percentage (± SD) of initial activity of reduced proteins (n = 3). (B) Incubation of CrTPI and CrICL in the presence of GSSG. Reduced proteins (left side, CrTPI; right side, CrICL) were incubated for 60min in the presence of 2mM GSSG (black bars). The reversibility of CrTPI and CrICL inactivation was assessed by incubation in the presence of 20mM DTT (white bars). Data are represented as mean percentage (± SD) of initial activity of reduced proteins (n = 3). Molecular Plant 2014 7, 101-120DOI: (10.1093/mp/sst139) Copyright © 2013 The Authors. All rights reserved. Terms and Conditions

Figure 9 Analysis of CrTPI and CrICL Glutathionylation with BioGSSG. CrTPI and CrICL were incubated for 1 h in the presence of BioGSSG (2mM) with or without prior incubation with 100mM IAM. Proteins were resolved by non-reducing SDS–PAGE and transferred to nitrocellulose for Western blotting with anti-biotin antibodies. The Red Ponceau (RP) staining of the membrane shows equal loading in each lane. The reversibility of the BioGSSG-dependent biotin signal was assessed by treatment with 20mM reduced DTT for 30min as indicated. Molecular Plant 2014 7, 101-120DOI: (10.1093/mp/sst139) Copyright © 2013 The Authors. All rights reserved. Terms and Conditions

Figure 10 Effect of GSNO on the Activity and Nitrosylation State of CrTPI. (A) Inactivation of CrTPI in the presence of GSNO. Reduced CrTPI (1 μM) was incubated with 2mM GSNO. At indicated times, aliquots of the incubation mixtures were withdrawn and the remaining TPI activity was determined (black bars). The reversibility of TPI inactivation was assessed by incubation for 15min in the presence of 20mM DTT (white bars). Data represent the mean percentage ± SD (n = 3) of TPI activity measured after 30- or 60-min incubation under control conditions. (B) CrTPI (25 μM) was treated for 30min in the presence of 5mM GSNO and nitrosylation was visualized using the biotin-switch technique followed by anti-biotin Western blots as described in the ‘Methods’ section. The Coomassie brilliant blue (CBB) staining of the gel shows equal loading in each lane. Molecular Plant 2014 7, 101-120DOI: (10.1093/mp/sst139) Copyright © 2013 The Authors. All rights reserved. Terms and Conditions