SUPPLEMENTARY INFORMATION

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1 SUPPLEMENTARY INFORMATION doi: /nature11403 Supplementary Methods Cell culturing and protein purification Cell culture and protein preparation methods have been described previously 20. Uptake of [ 14 C] betaine was measured in E. coli MKH13 cells 21. E. coli DH5αmcr 22 were used for the heterologous expression of strep-betp. Cells were grown at 37 C in LB medium supplemented with carbenicillin (50 µg/ml) and induction was initiated with anhydrotetracycline (200 µg/l). Cells were harvested at 4 C by centrifugation and resuspended in buffer containing 100 mm Tris-HCl (ph 8) and protease inhibitor Pefabloc 0.24mg/ml. Membranes were isolated from disrupted cells and solubilized with 2.5% β-dodecyl-maltoside (DDM) when purified protein was subsequently crystallized, or 1.3% of the same detergent when protein was reconstituted. The protein was then loaded on a StrepII-Tactin macroprep column, washed with 50 mm Tris-HCl (ph 7.5), 500 mm NaCl, 8.6 % Glycerol, % DDM, and eluted with 5 mm desthiobiotin, 50 mm Tris-HCl (ph 7.5), 200 mm NaCl, 8.7% glycerol and 0.6% Cymal-5, if used for crystallization, or 0.05 % DDM if used for reconstitution. Prior to crystallization the protein was loaded onto a Superose 6 (GE Healthcare) size-exclusion column equilibrated with 20 mm Tris-HCl (ph 7.5), 200 mm NaCl and 1.2% Cymal-5. This purified protein was concentrated at 4 C to approx. 10 mg/ml at 3000 g in a Vivaspin tube (Vivascience) with a 100k -molecularweight cut-off, and incubated for 16 hours at 4 C with either 1mM choline or 5mM betaine. 1

2 RESEARCH SUPPLEMENTARY INFORMATION Site-directed mutagenesis Site-directed mutagenesis of the pask-iba5betp 20 and pask IBA7betPΔN29/E44E45E46/AAA 23 plasmids were performed using QuickChangeTM kit (Stratagene), Pfu Turbo DNA polymerase, and specific Oligonucleotides (Table S3). The mutations were verified by nucleotide sequencing. The fully functional mutant BetP-ΔN29/E44E45E46/AAA 23 was used for crystallization purposes yielding in improved diffraction power and isotropy of the crystals. Crystallization and structure determination BetP-ΔN29/E44E45E46/AAA and BetP-ΔN29/E44E45E46/AAA/G153D were cocrystallized with 5mM betaine and 1mM choline, respectively, at 18 C by vapour diffusion in hanging drops of 1.5 µl protein solution with 1.5 µl of 100 mm Na-tricitrate (ph ), 100 mm NaCl, 17 24% PEG 400 as reservoir solution. Crystals of BetP-ΔN29/EEE44/45/46AAA /G153D diffracted to 3.2 Å and data were collected on the beamline id29 at the ESRF (European Synchrotron Radiation Facility, Grenoble France). Crystals of BetP-ΔN29/E44E45E46/AAA diffracted to 3.1 Å and data were collected on the Max Planck beamline X10SA at the SLS (Swiss Light Source at the Paul Scherrer Institut, Villigen - Switzerland). Data were processed using the XDS package 24 and the anisotropy was corrected on the UCLA Diffraction Anisotropy Server ( 25. Structures were determined by molecular replacement with BetP (PDB entry 3P03 and 4AMR) as search models using PHASER 26 and refinement was performed using PHENIX 27 combined with manual rebuilding in COOT

3 SUPPLEMENTARY INFORMATION RESEARCH Protein reconstitution into liposomes Functional reconstitution of BetP and mutants was performed as described 20. Briefly, liposomes (20 mg phospholipid/ml) from E. coli polar lipids (Avanti polar lipids) were prepared by extrusion through polycarbonate filters (100 nm pore-size) and diluted 1:4 in buffer (250 mm KPi ph 7.5). After saturation with Triton X-100, the liposomes were mixed with purified protein at a lipid/protein ratio of 10:1 (w/w). BioBeads at ratios (w/w) of 5 (BioBeads/Triton X-100) and 10 (BioBeads/DDM) were added to remove detergent. Finally, the proteoliposomes were centrifuged and washed before being frozen in liquid nitrogen and stored at -80 C. Transport assays Uptake of [ 14 C] betaine in E. coli MKH13 cells was performed as described 29, E. coli MKH13 cells expressing a particular strep-betp mutant were cultivated at 37 C in LB medium containing carbenicillin (50 µg/ml), and induced at a OD 600 of 0.5 by adding anhydrotetracycline (200µg/l). After 2 h the cells were harvested and washed in buffer containing 25 mm KPi buffer (ph 7.5), 100 mm NaCl, then resuspended in the same buffer containing 20 mm glucose. For uptake measurements the external osmolality was adjusted with KCl. Cells were incubated for 3 minutes at 37 C before the addition of different concentrations of [ 14 C] betaine. Betaine uptake was measured at various time intervals within 1.5 minutes from which cell samples were passed through glass fiber filters (APFF02500, Millipore, Schwalbach, Germany), and washed twice with 2.5 ml of 0.6 M KPi buffer. The radioactivity retained on the filters was quantified by liquid scintillation counting. Immuno-blotting against the N- 3

4 RESEARCH SUPPLEMENTARY INFORMATION terminal StrepII-tag of the different BetP variants in membranes of E. coli MKH13 using StrepII-TAG specific antibody confirmed that mutant forms of BetP were synthesized to approximately the same level in cells. The kinetic constants were derived by Michaelis-Menten curve fitting of the uptakes rates versus the substrate concentration with GraphPad Prism version 5.0c for Mac OS X, GraphPad Software 30. Tryptophan fluorescence-binding assay Binding assays were performed with 100 µg/ml of purified BetP in proteoliposomes 31. Betaine concentrations ranged from 0.05 to 15 mm. Tryptophan fluorescence emission between 315 and 370 nm was recorded on a Hitachi F-4500 fluorescence spectrophotometer and averaged over four readings, with the excitation wavelength set to 295 nm and a slit width of 2.5 or 5.0 nm for excitation or emission respectively, at a constant NaCl concentration of 300 mm. Titration of proteoliposomes with NaCl was performed at a constant betaine concentration of 2 mm. The mean value and standard deviation at the 342 nm emission maximum was plotted for each substrate concentration. Binding constants were derived by fitting with the program GraphPad Prism version 5.0c for Mac OS X, GraphPad Software

5 SUPPLEMENTARY INFORMATION RESEARCH Supplementary Discussion Conformationally asymmetric trimers Structures of BetP-ΔN29/E44E45E46/AAA (PDB entry 4AIN) and BetP- ΔN29/E44E45E46/AAA/G153D (PDB entry 4DOJ) were solved by molecular replacement and subjected to iterative model building and refinement of each polypeptide chain in the BetP trimer (Table S1). Protomers A and B in BetP- ΔN29/E44E45E46/AAA/G153D (Fig. 1 and Fig. S3) capture a substrate-free outward-occluded (C eoc ) and a substrate-free outward-open state (C e ), respectively. Protomer C is in an inward-open state in complex with choline (C i S), which was already observed in a previous study (PDB entry 3P03) 32. Protomers A and B in BetP- ΔN29/E44E45E46/AAA (Fig. 1 and Fig. S3) adopt a closed conformation with distinct main chain changes in comparison to the inward-open and outward-open states. Protomer A shows a closed substrate-free state (C c ) and protomer B a closed substrate-bound state (C c S). The latter is characterized by a central binding site that is closed by nearly 14 Å of protein bulk from either side of the membrane. The betaine location observed here is significantly different from that in the inward-open (protomer C) or inward-occluded 23 state (PDB entry 2WIT). Again, Protomer C is in an inward-open state in complex with betaine (C i S). Crystal contacts The cytoplasmic loops of protomer C interact with the neighbouring C-terminal domain of protomer A, which in turn is also involved in crystal contacts (Fig. S3c-d). It appears that the formation of the inward-facing conformation observed in protomer C in both structures is triggered by this interaction, while the conformations of A and B depend entirely on the amount of substrate available during crystallization. 5

6 RESEARCH SUPPLEMENTARY INFORMATION Increasing amount of betaine during crystallization of BetP up to saturating conditions of 5 mm favours a closed conformational state, while concentrations below or close to 1 mm of choline during crystallization of BetP-G153D favoured an outward-facing conformation. To date we can only speculate about the functional meaning of conformational asymmetry trapped in the 3D crystals. As we observed asymmetry already in membrane-embedded BetP 33,34, we rule out crystal contacts which differ completely in 2D and 3D crystals. To date there is no evidence that consecutive cycling through the transporter states is involved in activity regulation, as it was suggested for the E. coli multidrug exporter AcrB 35, although it is tempting to speculate that this might be the case. Importance of rocking bundle and gating in the alternating-access mechanism of BetP In order to investigate the opening of the gates and subsequently the pathway during the cycle, we constructed a chimeric model combining the periplasmic gates (TMH6a and TMH10 ) of the outward-facing structure with the rest of the inwardfacing structure. This model shows that opening of the periplasmic gates alone is not enough to open a funnel (Fig. S10a). The same is observed when the scaffold (TMH3-4 and TMH8-9 ) of the outward-facing structure is combined with the rest of the inward-facing structure (Fig. S10b). However, when both periplasmic gates and scaffold are used in the model we observe a funnel (Fig. S10c). This indicates that both rocking-bundle and gating movements have to be present to open up the pathways in BetP. 6

7 SUPPLEMENTARY INFORMATION RESEARCH Supplementary Tables Table S1. Data collection and refinement statistics. Data collection PDB entry 4AIN PDB entry 4DOJ Space group P P Cell dimensions a, b, c (Å) , , , , α, β, γ ( ) 90, 90, 90 90, 90, 90 Resolution (Å) a ( ) ( ) R merge a 0.17 (0.54) 0.10 (0.32) I/σI a 10.1 (3.4) 14.8 (5.9) Completeness (%) a 81.2 (26.3) 86.0 (23.4) Refinement Resolution (Å) No. reflections R work /R free (%) 22.54/ /29.69 R.m.s.d. b bonds (Å) R.m.s.d. angles ( ) a Values in parentheses refer to data in the highest resolution shell. Statistics as reported by UCLA Diffraction Anisotropy Correction Server ( 25 after ellipsoidal correction b R.m.s.d., root mean square deviation. 7

8 RESEARCH SUPPLEMENTARY INFORMATION Table S2. Kinetic parameters from betaine transport and binding of WT BetP and mutants. K m µm V max nmol/min x mg cdw WT 13.2 ± ± 10.2 F156A 27.0 ± ± 7.2 F369G 70.0 ± ± 9.7 W373A ± ± 6.8 W374A 24.1 ± ± 2.9 W377A BD a BD F380A 8.1 ± ± 6.1 F384A 5.8 ± ± 3.0 K d mm B max (ΔF/F) WT 1.16 ± ± 0.02 F156A ± ± 0.09 F369G ± ± 0.02 W373A ± ± 0.03 W374A 62.9 ± ± 0.04 F380A 5.42 ± ± 0.02 F384A 6.20 ± ± 0.03 a Below detection (BD). 8

9 SUPPLEMENTARY INFORMATION RESEARCH Table S3. Sense primer sequences. Exchanged codons are underlined. Mutation Sequence 5-3 G153D F156A S306A M310A F369G W373A W374A W377A F380A F384A GCA GGT ATG GGT ATT GAT TTG ATG TTC TAC GGA GGT ATT GGT TTG ATG GCC TAC GGA ACC ACA GAA GGA ATC CAG TAC CTC GCC AAC GCC AAC ATG CTC TCC AAC GCC AAC GCG GTT CTG GCA GCT CTG GGT AGC TGG ACC ATC GGC TAC TGG GCA TGG TGG ATC TTC TAC TGG GCA GCG TGG ATC TCT TGG TCA TAC TGG GCA TGG GCG ATC TCT TGG TCA CCA GCA TGG TGG ATC TCT GCC TCA CCA TTC GTA GGA ATC TCT TGG TCA CCA GCC GTA GGA ATG TTC TTG GGT ATT GGT TTG ATG GCC TAC GGA ACC ACA GAA 9

10 RESEARCH SUPPLEMENTARY INFORMATION Supplementary Figures 7 1 H CT Figure S1. BetP topology with LeuT TMH numbering. Bundle domain in red (TMHs 1, 2, 6 and 7 ), hash motif in blue (TMHs 3, 4, 8 and 9 ), thin gates in green (TMHs 5 and 10 ) and TMHs (-2) and (-1) together with helix 7 (H7) and the C- terminal domain (CT) are shown in grey. 10

11 SUPPLEMENTARY INFORMATION RESEARCH Relative ΔF/F percentage BetP WT BetP-G153D [Na + ], mm Figure S2. Tryptophan fluorescence of BetP WT and BetP-G153D dependent on the sodium concentration. The maximum of tryptophan fluorescence at 340 nm as a function of sodium concentration was measured in proteoliposomes at a constant concentration of 2 mm betaine. Kinetic parameters for BetP WT are K d = ± 4.0 mm, n Hill = 1.9 ± 0.1. Kinetic parameters for BetP-G153D are K d = 25.0 ± 1.5 mm, n Hill = 1.8 ± 0.2. Each point shows the average of at least three independent experiments. The error bars represent the standard deviation (s.d.). 11

12 RESEARCH SUPPLEMENTARY INFORMATION a b Ce BetP-G153D!"# B A C!"%&# CcS BetP B A C c!"%&$# C is Ceoc!&#!&$#!'%&#!'%&$#!' # Cc!"$#!'$# C is d Figure S3. (a) Conformational states of BetP protomers in the trimers. BetP-G153D (PDB entry 4DOJ), Chain A; outward-occluded apo state (Ceoc). Chain B; outwardopen apo state (Ce). Chain C; substrate-bound inward-open state (CiS). BetP (PDB entry 4AIN), Chain A; closed apo state (Cc). Chain B; substrate-bound closed state (CcS). Chain C; substrate-bound inward-open state (CiS). (b) 10 conformational states in the alternating-access cycle. (c) and (d) show crystal contacts of PDB entries 4AIN W W W. N A T U R E. C O M / N A T U R E

13 SUPPLEMENTARY INFORMATION RESEARCH and 4DOJ, respectively. The C-terminal domain of protomer A establishes the main crystal contacts. 13

14 RESEARCH SUPPLEMENTARY INFORMATION W374 TMH6! "#$ %& W377! " %& W194 TMH1 Figure S4. Superposition of the betaine-binding site in the C i S state (dark colours) and C ioc S from PDB entry 2WIT (light colours). 14

15 SUPPLEMENTARY INFORMATION RESEARCH a b Betaine uptake rate [nmol/(min x mg cdw)] 250 WT F156A F369G W373A W377A W374A!F/F WT W373A W374A F369G F156A c [Betaine] µm!"#$%&!"#'%& [Betaine] mm 140$ TMH1 145$ 150$ 155$ 160$!"#$%!&$'% (&)&% (&)*% (&))%!&+,%!&+*% 365$ TMH6 370$ 375$ 380$ 385$ d e Betaine uptake rate [nmol/(min x mg cdw)] WT F380A F384A!F/F WT F380A F384A [Betaine] µm [Betaine] mm Figure S5. Mutagenesis analysis of aromatic residues in the substrate pathway. Uptake rates in nmol per min and mg cell dry weight (cdw) were measured dependent on the betaine concentration in E. coli MKH13 cells expressing BetP mutants of aromatic residues in the periplasmic (a) and cytoplasmic (d) pathways. The maximum of tryptophan fluorescence at 340 nm dependent on betaine concentration was measured in proteoliposomes for mutants of aromatic residues in the periplasmic (b) and cytoplasmic (e) pathways. Each point shows the average of at least three 15

16 RESEARCH SUPPLEMENTARY INFORMATION independent experiments. The error bars represent s.d. (c) Location of aromatic residues in the substrate pathway in a BetP protomer. TMH1 and TMH6 in red. Sequence alignment of conserved aromatic residues in TMH1 and TMH6 in several symporters from the BCCT family. BetP from Corynebacterium glutamicum is aligned with: OpuD from Bacillus subtilis, EctP from Corynebacterium glutamicum, LcoP from Corynebacterium glutamicum, BetU from Escherichia coli and BetL from Listeria monocytogenes. In yellow are the residues forming the tryptophan prism in the S1-site, in blue the rest of the aromatic residues lining the substrate pathway. TMH6' W374 W373 TMH3'! W377 "#! " #$ Figure S6. Tryptophan-prism remains nearly unaltered in the C c and C c S states. Betaine molecule is shown in black, red and blue. 16

17 SUPPLEMENTARY INFORMATION RESEARCH a Ceoc Ce Na2 Na2 b TMH1' TMH10' TMH6' Figure S7. Comparison of the Ce and Ceoc states. (a) Surface representation of the Ce state shows full accessibility to the Na2-site (purple sphere) while in the Ceoc state Trp377 occludes the site. (b) Superposition of Ceoc (light blue) and Ce state (colors as in Fig. S1). The tryptophan-prism is displayed in sticks. Both structures superpose with an r.m.s.d. of 1.3 Å. 17 W W W. N A T U R E. C O M / N A T U R E 1 7

18 RESEARCH SUPPLEMENTARY INFORMATION Transporter, Periplasmic,view, Cytoplasmic,view, BetP% 5, 7, 2, 1, 6, 5, 4, 8, 9, 3, 8, 3, 4, 10, 9, 1, 6, 7, 2, 10, LeuT% 7, 5, 8, 3, 2, 1, 4, 6, 10, 9, 9, 4, 8, 5, 6, 1, 2, 7, 10, 3, Mhp1% 5, 2, 7, 8, 3, 1, 4, 4 6, 10, 9, 5, 1, 4, 9, 8, 6, 2, 7, 3, 10, Figure S8. Alternating access in BetP, LeuT and Mhp1. Periplasmic and cytoplasmic views of the superposition of the outward-open and inward-open conformations of BetP, LeuT and Mhp. The outward-facing structures are coloured as in Fig. S1. The inward-facing structures are shown in salmon for the bundle domain, light blue for the hash motif and light green for the thin gates. 18

19 SUPPLEMENTARY INFORMATION RESEARCH TMH8 TMH7 TMH4 TMH1 TMH2 TMH9 Na2 Na1 TMH6 TMH3 Figure S9. The two sodium-binding sites are located in the interface between bundle and scaffold domains in BetP. Bundle and scaffold TMH are colored in red and blue, respectively. Sodium ions at the Na2 and Na1 sites are colored in purple. 19

20 RESEARCH SUPPLEMENTARY INFORMATION a b c Figure S10. Chimeras models that combine (a) the periplasmic gates (TMH6a and TMH10 ) of the outward-facing structure with the rest of the inward-facing structure, (b) the scaffold (TMH3-4 and TMH8-9 ) of the outward-facing structure and the rest of the inward-facing structure and (c) both, periplasmic gates and scaffold of the outward-facing structure and the rest of the inward-facing structure. 20

21 SUPPLEMENTARY INFORMATION RESEARCH Supplementary Movie Movie Legend: The movie represents structural morphs of the conformational changes in BetP during transition from the outward-open to closed and inward-open states. Bundle helices (TMHs 1 and 6 ) are in red, the hash motif (TMHs 3, 4, 8 and 9 ) is in blue and thin gates (TMHs 5 and 10 ) are in green. TMHs (-2) and (-1) together with helix 7 (H7) and the C-terminal domain (CT) are shown in grey. 21

22 RESEARCH SUPPLEMENTARY INFORMATION References 20. Rubenhagen, R., Ronsch, H., Jung, H., Kramer, R. & Morbach, S. Osmosensor and osmoregulator properties of the betaine carrier BetP from Corynebacterium glutamicum in proteoliposomes. J Biol Chem 275, (2000). 21. Haardt, M., Kempf, B., Faatz, E. & Bremer, E. The osmoprotectant proline betaine is a major substrate for the binding-protein-dependent transport system ProU of Escherichia coli K-12. Mol Gen Genet 246, (1995). 22. Grant, S.G., Jessee, J., Bloom, F.R. & Hanahan, D. Differential plasmid rescue from transgenic mouse DNAs into Escherichia coli methylation-restriction mutants. Proc Natl Acad Sci U S A 87, (1990). 23. Ressl, S., Terwisscha van Scheltinga, A.C., Vonrhein, C., Ott, V. & Ziegler, C. Molecular basis of transport and regulation in the Na(+)/betaine symporter BetP. Nature 458, (2009). 24. Kabsch, W. Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants. Journal of Applied Crystallography 26(1993). 25. Strong, M. et al. Toward the structural genomics of complexes: crystal structure of a PE/PPE protein complex from Mycobacterium tuberculosis. Proc Natl Acad Sci U S A 103, (2006). 26. McCoy, A.J. et al. Phaser crystallographic software. J Appl Crystallogr 40, (2007). 27. Terwilliger, T.C. et al. Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard. Acta Crystallogr D Biol Crystallogr 64, 61-9 (2008). 28. Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 60, (2004). 29. Ott, V., Koch, J., Spate, K., Morbach, S. & Kramer, R. Regulatory properties and interaction of the C- and N-terminal domains of BetP, an osmoregulated betaine transporter from Corynebacterium glutamicum. Biochemistry 47, (2008). 30. Motulsky H. Analyzing Data with GraphPad Prism, GraphPad Software Inc., San Diego CA, (1999). 31. Ge, L., Perez, C., Waclawska, I., Ziegler, C. & Muller, D.J. Locating an extracellular K+-dependent interaction site that modulates betaine-binding of the Na+-coupled betaine symporter BetP. Proc Natl Acad Sci U S A 108, E890-8 (2011). 32. Perez, C. et al. Substrate specificity and ion coupling in the Na+/betaine symporter BetP. EMBO J 30, (2011). 33. Ziegler, C. et al. Projection structure and oligomeric state of the osmoregulated sodium/glycine betaine symporter BetP of Corynebacterium glutamicum. J Mol Biol 337, (2004). 34. Tsai, C.J. et al. Structural asymmetry in a trimeric Na+/betaine symporter, BetP, from Corynebacterium glutamicum. J Mol Biol 407, (2011). 35. Seeger, M.A. et al. Structural asymmetry of AcrB trimer suggests a peristaltic pump mechanism. Science 313, (2006). 22