Transient Ribosomal Attenuation Coordinates Protein Synthesis and Co-translational Folding

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1 SUPPLEMENTARY INFORMATION: Transient Ribosomal Attenuation Coordinates Protein Synthesis and Co-translational Folding Gong Zhang 1,2, Magdalena Hubalewska 1 & Zoya Ignatova 1,2 1 Department of Cellular Biochemistry, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, Martinsried, Germany 2 Department of Biochemistry, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str 24-25, Potsdam-Golm, Germany Address correspondence to Zoya Ignatova, ignatova@uni-potsdam.de

2 Supplementary Figure 1 Putative slow-translating regions are more frequent in Tat-secreted proteins of Bacillus subtilis. The open-reading frames of the secreted proteins from B. subtilis proteome were extracted based on the predictions of the SignalP 3.0 server ( and separated into two groups: exported via the Tat (Tat) or Sec (Sec) pathway.

3 Supplementary Figure 2 Determination of translation competency, translation yields, and the conditions for proteinase K digestion. (a) The discrete intermediates of SufI translation in vitro are products of transient translational attenuation as short ribosome-bound fragments were translationally competent (left autoradiogram) and puromycin-sensitive (right autoradiogram). The RNCs of in vitro translated SufI were isolated by sucrose cushion (lane 1, left panel) and added to a fresh batch of synchronized E. coli cell-free translation mixture containing all non-radioactive amino acids and incubated for 2 h at 30 C (lane 2, left panel). The transiently stalled translational intermediates were able to continue translation to a full-length (FL) product. In addition, transiently staled intermediates were stably tethered to the ribosomes as suggested by their sensitivity to puromycin. To RNCs isolated by sucrose cushion (SC) (lane 2, right panel) of in vitro translated SufI (lane 1, right panel) puromycin to a final concentration 2 mm was added and further incubated for 4 h (lane 4, right panel). After a subsequent second isolation of the RNCs (lane 5, right panel) all transient intermediates were released from the ribosomes. To prove the spontaneous release of the nascent chains from the ribosomes during the incubation time, isolated RNCs were incubated under same conditions without puromycin and no substantial intensity changes in the autoradiogram pattern were detected (lane 3, right panel).

4 Mw, molecular weight marker. (b) Optimization of the proteinase K digestion. RNCs isolated by sucrose cushion from the SufI in vitro translation system were subjected to digestion with 10 ng/µl proteinase K on ice for different times. Note that the optimal time for limited proteolysis of SufI was five minutes. (c) Transcription was unaffected by the silent mutations. The concentration of each transcript was determined using quantitative reverse transcription (for details see Supplementary Methods). Lanes: 1 - DNA fragment markers in base pairs (bp); 2 - wild-type SufI; 3 -SufI-Δ ; 4 -SufI-Δ ; 5 - SufI-3R

5 Supplementary Figure 3 Penicillin amidase (PA) is translated via many transient intermediates. Synchronized pulse-translation (left autoradiogram) of S 35 -labeled full-length (FL) PA or PA chains truncated down-stream of the kda (marked with ) and kda (marked with Δ) yielded many transiently arrested fragments, whose sizes matched the predicted minima in the translation rate profile (underlined and highlighted with corresponding symbols). The predicted slow-translating clusters delineate single structural domains in PA (pdb access code 1PNK); the corresponding transiently stalled intermediates were largely protease K resistant (+PK, right autoradiogram) suggesting that they have already acquired higher order structure while still tethered to the ribosomes. PA and the truncated variants were translated from the pivex 2.3d plasmid under the control of thet7 promoter.

6 Supplementary Figure 4 Bacterial Hsp70/40 (DnaK/DnaJ) chaperones do not bind to the nascent chains of wild-type SufI. SufI was translated in the coupled transcription-translation E. coli cell-free system, and the RNC-complexes were isolated by sucrose cushion (SC). For comparison, a control reaction with empty vector without the SufI-insert and the isolated RNCs-fraction was loaded. All samples were resolved on 15% SDS-PAGE and subsequently blotted with monoclonal anti-dnak (1:2000 dilution; Stressgen) and polyclonal anti-dnaj (1:5000 dilution; Stressgen) antibodies.

7 Supplementary Figure 5 SufI unfolds upon chemical denaturation in a domain-wise manner. (a) SufI unfolds via well defined biphasic transition between 3.5 and 5 M urea, implying the presence of a stable unfolding intermediate(s) with retained degree of native Trp-fluorescence. The standard deviations were determined from three independent experiments. (b) Unfolding intermediate(s) are enriched at the same urea concentrations as suggested from the dependence of the amplitude of the kinetic traces on the urea concentrations. The SufI unfolding curves at various urea concentrations (plotted at the X-axis) showed a double-exponential behavior, dominated by an initial fast unfolding phase with amplitude plotted on the Y-axis. (c) Native SufI is relatively resistant to treatment with proteinase K up to 1M urea. In the course of unfolding, proteinase K released fragments of various lengths, some of which matched the size a single domain or various combinations of them. The domain architecture based on the primary amino acid sequence is schematically presented and the same color code is used to mark the proteolytically stable bands. Mw, molecular weight marker.

8 Supplementary Figure 6 Elimination of only one slow-translating codon is not sufficient to completely abolish the co-translational folding of full-length SufI. Leu244 (Δ ) or Leu252 (Δ ) were silently mutated to a CUG codon that is read by a highly abundant trna and the in vitro translated full-length (FL) protein was significantly proteinase-resistant. SC denotes RNCs isolated by sucrose cushion and PK limited digestion by proteinase K.

9 Supplementary Table 1 Mass-spectrometry analysis of the RNCs from the in vitro translation mixture translating SufI or empty vector. Protein name a SufI Empty vector Mascot score rpsa 30S ribosomal subunit protein S rpsb 30S ribosomal subunit protein S rpll 50S ribosomal subunit protein L7/L rple 50S ribosomal subunit protein L rpsm 30S ribosomal subunit protein S rpli 50S ribosomal subunit protein L rplf 50S ribosomal subunit protein L rpse 30S ribosomal subunit protein S rpsc 30S ribosomal subunit protein S rpsd 30S ribosomal subunit protein S rplo 50S ribosomal subunit protein L rpsg 30S ribosomal subunit protein S rplv 50S ribosomal subunit protein L rplk 50S ribosomal subunit protein L rpld 50S ribosomal subunit protein L tig Trigger factor, protein folding chaperone dnak Hsp70 molecular chaperone, heat-inducible Suf I a Both reactions did not differ in the content of the constitutive ribosomal components; representative examples of some ribosomal proteins are shaded.

10 SUPPLEMENTARY METHODS Quantitative determination of mrna. Translation reactions of wild-type SufI, SufI-Δ 25-28, SufI-Δ 33-40, and SufI-3R 25-28, containing 2.5 ng plasmid DNA were transcribed for 15 min at 30 C in a 25 µl reaction mixture of the in vitro translation kit (without addition of amino acid mix). The samples were diluted 50-fold and treated with 0.75 U DNAse at 37 C for one hour to digest the plasmid DNA and various dilutions of the samples were subjected to quantitative RT-PCR with SufI specific primers. No fragment was amplified when primers outside of the SufI coding region were used. In vitro unfolding experiments. C-terminally His 6 -tagged SufI was expressed in E. coli BL21(DE3) cells from the pet28b plasmid. The expression was induced at OD 600 =2 by adding 0.8 mm IPTG for 3 h at 37 C. Cells were lysed and SufI was affinity purified from the soluble fraction using a Ni-NTA column as described by the manufacturer (Qiagen). Protein concentration was determined spectrophotometrically using the theoretical ε 280 value of M -1 cm µm pure SufI dissolved in 10 mm Tris.HCl, ph 8.0 containing increasing concentrations of urea was incubated for 3 h at room temperature. Equilibrium urea-unfolding was monitored by the intrinsic Trp fluorescence (excitation 280 nm; 5 nm bandwidth) and emission spectra between 300 and 400 nm or time-resolved emission changes at 350 nm were recorded on a Fluorolog (Horiba/Jobin Ivon) fluorometer equipped with a thermoelectric cell holder. Concentrated solution of pure SufI was rapidly diluted to a final concentration of 1.4 µm into 10 mm Tris.HCl, ph 8.0 containing various concentrations of urea and the unfolding kinetics were recorded at 37 C at 350 nm (5 nm bandwidth; excitation 280 nm; 5 nm bandwidth). The unfolding rate constants and the amplitudes were obtained by exponential curve fitting using the software package SigmaPlot. The exact final urea concentrations were calculated from the refractive index. In addition, the unfolding of SufI was monitored by partial proteinase K digestion. 4 µm purified SufI was incubated in 10 mm Tris.HCl, ph 8.0 containing increasing urea concentrations from 0 to 4 M at 25 C for 3 h and subsequently subjected to partial proteolytic digestion with 10 ng/µl proteinase K for 5 min on ice. The proteolytic fragments were resolved on 15 % SDS-PAGE and visualized by Coomassie staining.