Linck R , Fu X , Lin J , Ouch C , Schefter A , Steffen W , Warren P , Nicastro D .

R01 GM083122 NIGMS NIH HHS , GM083122 NIGMS NIH HHS

	FIGURE 1. Summary of previously proposed locations of Ribbons of PFs. PFs (black) and tektin fibrils/filament (green) are shown. A, A-tubule; B, B-tubule; IJ, inner junction; PFs numbered according to Ref. 58. The approximate location and shape of the partition-associated material (stippled) is redrawn from Ref. 59 and likely contains the MIP4 density (11). a, the 3-PF Ribbon was originally suggested to arise from the PFs forming the partition between the A- and B-tubules (12). b–e, given the unknown structure of the A-tubule/B-tubule junctions prior to tannic acid fixation (60) and the lack of three-dimensional information about the origin of these PFs, it was uncertain whether the stable Ribbon corresponded to PFs A10-11-12 (data not shown) or to PFs A11-12-13 (b), or PFs A12-13-1 (c), or whether there were two kinds of Ribbons. Several observations pointed to a different or second location of Ribbon PFs closer to the inner dynein arms (see “Discussion”), e.g. PFs A13-1-2 (d) or PFs A1–3 (e). f–h, different locations have also been proposed for tektins, i.e. f, the IJ structure or thin fibrils either between PFs or in the grooves between PFs (15, 27, 32, 61), or g, the partition material on the A-lumen side of tubulin PFs A11-12-13-1 (redrawn from Ref. 62), or h, one of the PFs of the Ribbon (15, 44, 63).
	FIGURE 2. Structure of intact and fractionated DMTs. a–d, three-dimensional structure of an intact sea urchin (S. purpuratus) flagellar DMT obtained by cryo-ET and subtomogram averaging of the 96 nm axonemal axial repeats (1200 repeats; resolution in the center of the volume is 3.3 nm). The DMT is shown as tomographic slices (a and b) and isosurface renderings (c and d) in cross-sectional (a and c) and longitudinal (b and d) views. For clarity, the dynein arms and radial spokes were removed, and only the DMT core is shown. A, A-tubule; B, B-tubule; PFs are numbered; IJ, inner junction protein(s); microtubule inner protein MIP1, blue; MIP2, red; MIP3, yellow; stippled area marks the thickened, non-tubulin partition-associated material (p); diagonal line in c demarcates the viewing angle in b and d. DMTs and fractions are either viewed from the proximal (−) to the distal (+) end of the DMT in cross-section (a and c) or oriented with the proximal end to the left (b and d). Scale bar, 10 nm for a–d. See also supplemental Movie S1. e–i, negative stain EM specimens (S. purpuratus) corresponding to the fractions shown in Fig. 3: e, DMT composed of A- and B-tubules. f, A-tubule with remnant PF(s) (arrow) of the B-tubule corresponding to PFs B9 and B10 that are tightly associated with the A-tubule by the IJ proteins. g, Sarkosyl Ribbon typically composed of three PFs here (white lines) or four PFs from L. pictus (data not shown). h and i, tektin filaments measuring ∼5 nm wide and up to several microns long, composed of tektins A, B, and C (Fig. 4a, lane 3). Note that tektin filaments appear to be smooth, with no apparent lateral side projections. Scale bars, 100 nm for e–h, 200 nm for i.
	FIGURE 3. Quantitative fractionation of S. purpuratus axonemes and distribution of Ribbon proteins. a, axonemes were sequentially fractionated in discrete steps, and matched fractions were analyzed by SDS-PAGE (b), immunoblotting (c), and EM (Fig. 2). Numbers in parentheses are the percentages of protein in each fraction relative to axonemes (100%), referenced to BSA. b, SDS-PAGE of the fractions in a. The asterisk (Tektin B*) indicates the presence of co-migrating SpRib45, a homologue of CrRib43a (Fig. 4b). MWS, molecular weight standards. c, immunoblot analysis of identical replicas of the gel lanes in b, stained with the following antibodies (characterized in Fig. 4a): anti-SpRib74 + anti-SpRib85.5 (a mixture of the two separately specific antibodies); anti-tektin consensus peptide against the sequence RPNVELCRD, present in most tektins from echinoderms to humans; anti-tektin A; anti-tektin B; and anti-tektin C. The anti-consensus peptide shows that no polypeptides with this peptide, other than tektins A, B, and C, are present in any of the fractions; the uneven staining of the different tektins may be due to different and possibly interfering amino acid residues bordering the consensus sequence in the full-length polypeptide chains (30). Results: by densitometry, >95% of SpRib74/85.5 are retained in the Ribbon fraction (lane 6) but are completely solubilized along with all tubulin upon Sarkosyl-urea extraction (lane 9); and >95% of tektins are retained in Ribbons (lane 6). In the end, when Ribbons are extracted with Sarkosyl-urea, the resulting insoluble filaments (lane 8, Fig. 2h) are composed of tektins A, B, and C in equal molar amounts (Fig. 5a); a fraction of these tektins become soluble (lane 9). Tektin A and B bands are distorted and do not line up precisely in the heavily loaded lanes, because they are “pushed” ahead by the larger amount of nearly co-migrating tubulin.
	FIGURE 4. Composition of Ribbons, characterization of antibodies, and two-dimensional PAGE for MS analysis. a, lanes 1–3. SDS-PAGE protein staining of the following DMT fractions: lane 1, S. purpuratus Sarkosyl Ribbons (EM appearance shown in Fig. 2g) showing the principal constituent polypeptides; lane 2, ribbons partially extracted with urea to reduce tubulin that perturbs and obscures nearby bands; lane 3, Sarkosyl-urea-purified tektin filaments (Fig. 2h) composed of tektins A, B, and C. Masses as determined from their sequences are as follows: SpRib85.5, 85.5 kDa; SpRib74, 74 kDa; tektin A, 53 kDa; tektin B, 51 kDa; tektin C, 47 kDa; α- and β-tubulin, ∼50 kDa (*SpRib45 co-migrates with tektin B). Lanes 4–9 show immunoblots of S. purpuratus DMTs stained with the indicated antibodies. b, two-dimensional IEF/SDS-PAGE of Sarkosyl Ribbons. Major polypeptides (labeled) and spots 1–10 were reproducibly present and were cut out and analyzed by MALDI-TOF mass spectrometry (Table 2). Spots 1 and 2 were identified as SpRib45, homologue of Chlamydomonas CrRib43a. Corresponding positions of spots 3, 4/5, and 6/7 are indicated in a.
	FIGURE 5. Stoichiometry of Ribbon proteins. a, stoichiometry of tektins. Ribbons were extracted once with Sarkosyl-urea, leaving a residual amount of associated tubulin but minimizing the loss of tektin C, resolved by SDS-PAGE, and stained quantitatively with Serva Blue. Gel lanes were scanned, and the stain intensities of α-tubulin and tektins A, B, and C measured. Because β-tubulin migrates closely with tektin B (Fig. 4a, lane 2) and because the moles of α-tubulin must equal the moles of β-tubulin, the stain intensity of α-tubulin was subtracted from the intensity of the (tektin B + β-tubulin) peak to determine the amount of tektin B alone. The intensities of tektins A, B, and C were divided by their masses (53, 51, and 47 kDa, respectively) to give intensity/kDa and normalized to tektin A. The molar ratio of tektins A/B/C was thus determined to be 1:1:1. Dashed lines indicate the separation of the intensities of the individual polypeptides, and the dotted lines indicate the registration of the respective polypeptides in b. b, stoichiometry of Ribbon proteins. DMTs were extracted once with Sarkosyl (to minimize sample loss) and analyzed as described for tektin filaments above. Dashed lines indicate the separation of the intensities of the individual polypeptides. The stoichiometry of the Ribbon proteins was thus calculated and reported in Table 1. c, the number of Ribbons per axoneme was estimated as follows. Reference lanes were loaded with the amount of axonemal tubulin calculated for one, two, and three Ribbons (of three tubulin PFs) per DMT (i.e. 11.6, 23.2, and 34.8%, respectively), against which the experimental Ribbon sample was compared. The α-tubulin region was measured (bracket, dashed lines) and plotted as % of axonemal α-tubulin versus the integrated (stain) intensity of α-tubulin, ■. The experimentally obtained Ribbon α-tubulin (+) corresponds to ∼14% of the axonemal α-tubulin, very close to the amount (11.6%) expected for one Ribbon of three tubulin PFs per DMT. The value 14.1% is probably artificially high and closer to the theoretical 11.6%, because (i) central pair-MTs are less stable than DMTs and therefore some central pair-tubulin is lost during the isolation of axonemes, and (ii) because a small percentage (<5%) of the once-extracted Ribbons contains four PFs and not three.
	FIGURE 6. Negative stain-EM and immuno-EM of DMT, Ribbon, and filament fractions. a, negatively stained preparation of a partially extracted DMT, showing a transition from DMT→A-tubule→Ribbon→A-tubule→Ribbon and one transition from A-tubule→Ribbon. A, A-tubule; B, B-tubule; R, Ribbon of four and then three PFs. b and c, Ribbon→filament transitions, negatively stained, showing the emergence of a single ∼5-nm wide tektin filament. R, Ribbon; F, filament. c, bracket shows the region of the transition, where the origin of the filament in the Ribbon is obscured (see also cryo-ET in Fig. 12); this could be due to remaining SpRib74, SpRib85.5, and/or tubulin adhering to the stable tektin filament as it emerges from the Ribbon. d, purified Ribbons (R) labeled with anti-SpRib85.5 primary antibody/gold-secondary antibody and negatively stained for EM. Some of the gold particles are indicated by arrowheads. Note that the tektin filaments (F) appearing in the field are not labeled with gold antibody. Scale bars, a, c, and d, 100 nm; b, 200 nm.
	FIGURE 7. Cryo-electron tomogram of a thermally fractionated, reconstructed, and averaged DMT. Labeled and unlabeled cross-slices (a and a′) and longitudinal slices (b and b′) of an A-tubule with B-tubule hook are shown. Plane of b and b′ is indicated by red line in a. a and a′, viewed from the proximal (minus) end to the distal (plus) end; b and b′, proximal end to the left. Shown are the following: A-tubule (A, with PFs A9 to A2 numbered); MIP2; pam/bracket, partition-associated material; and the remaining portion of the B-tubule (B), including the inner junction component(s) (IJ), PFs B9–10 and MIP3. These markers were used to identify the location of the stable protofilaments A11-12-13-1 (see Fig. 8). Scale bars, a, a′, b, and b′, 20 nm.
	FIGURE 8. Localization of the stable ribbon and SpRib74. a and b, negatively stained DMT→Ribbon transitions without (a) and with anti-SpRib74/immunogold labeling (b); inset at higher magnification. Anti-SpRib74 does not label intact DMTs or A-tubules, and instead it labels only the extending Ribbon along the side of the Ribbon facing the lumen of the A-tubule. c–h, immuno-cryo-EM (c) and immuno-cryo-ET (d–h) of DMT→Ribbon transitions after labeling with anti-SpRib74/immunogold (arrowheads). Isolated Ribbons (RC) that were added as a control are continuously labeled by the antibodies (see also Fig. 9). In DMT→Ribbon transitions, labeling only occurs along Ribbons and only along the side of the Ribbon facing the lumen of the A-tubule. d, red boxes and letters e–h along the DMT→Ribbon transition indicate where the cross-sectional slices in e–h are taken. The origin of the four stable Ribbon PFs (h) can be traced to PFs A11-12-13-1 of the A-tubule (e). The yellow arrow indicates the exact same anti-SpRib74/gold particle in d and g. Note that the shape of the partition-associated material appears to be altered somewhat in the extending Ribbon (g and h) from that in the intact A-tubule (e). i–k, models depicting the location of the partition material (i and j) and the same DMT→Ribbon transition in k as shown in d but with model superimposed over the EM structure, depicting the location of the stable Ribbon of PFs. All panels, A, A-tubule (magenta); B, B-tubule (blue); MIP2 (red); MIP3 (yellow); IJ protein (purple); R, Ribbons; arrowheads, immunogold particles; partition material, stippled orange. Cross-sections (e–h) and two-dimensional models (i and j) are viewed from the proximal (−) to the distal (+) end of the DMT→Ribbon transition; in longitudinal view (d and k) the proximal (−) end is toward the left, with polarity determined as in Fig. 7. Scale bars, a–d and k, 50 nm; e–h, 10 nm.
	FIGURE 9. Immuno-cryo-ET of DMT→Ribbon transitions. Tomographic slice of DMT→Ribbon transitions after immunolabeling with anti-SpRib74/gold antibody. The gold-antibody complexes heavily label both the Ribbon controls (RC) and Ribbons (R) emerging from the A-tubules but only on the side facing the lumen of the A-tubule. White arrowheads, gold particles; A, A-tubules; B, B-tubules. Scale bar, 100 nm.
	FIGURE 10. Ribbon→filament transitions immunolabeled with anti-tektin antibodies. The bare connecting or extending filaments are labeled by all three of the specific anti-tektin antibody/gold particles (marked by arrowheads), indicating that the single filament is composed of tektins A, B, and C; the statistics of the gold labeling are given in the text. a, nonspecific background labeling by gold is low (one of the few exceptions is labeled by an asterisk). Rarely do these antibodies/gold particles label Ribbons, indicating that the epitopes of tektins in the intact Ribbon are inaccessible to the antibodies. a–d, anti-tektin-A labeling of Ribbon→filament transitions. a, S. purpuratus Ribbons; b–d, L. pictus Ribbons. e–h, anti-tektin-B labeling of S. purpuratus Ribbon→filament transitions. i–p, anti-tektin-C labeling of L. pictus Ribbon→filament transitions. Scale bars, a, i, and j, 200 nm; b–h and k–p, 100 nm.
	FIGURE 11. Ribbon→filament transitions immunolabeled with anti-tubulin antibodies. Only the Ribbons (R) containing tubulin protofilaments are immunolabeled (arrowheads); the bare or extending filaments (F) are rarely labeled with anti-tubulin. The statistics of the gold labeling are given in the text. Scale bars, a–j, 100 nm.
	FIGURE 12. EM of Ribbon-filament transitions. a–c, Ribbon-filament transitions imaged by negative staining EM (a) and by cryo-ET (b) and modeled (c). In all cases, a single filament (as in Figs. 6, b and c, 10, and 11) appears to emerge from the middle of the Ribbon, as seen in two dimensions; however, the resolution in the z-direction of the ET data is not sufficient to locate the filament in/on the Ribbon in three dimensions unambiguously. d and e, cross-sectional view of a 24-nm thick slice through a subtomographic average of a Ribbon (d) and an isosurface rendering representation (e) reveals details of the partition-associated material (orange) asymmetrically bound to three Ribbon PFs (magenta); however, the structure of the partition material changes along its axis (see supplemental Movie S1). Comparison of these images with intact DMTs (Fig. 2, a and c) and immuno-cryo-ET images of DMT→Ribbon transitions (Fig. 8, d–h) localizes these three stable Ribbon PFs to either A11-12-13 or A12-13-1, with the ambiguity being due to the loss of polarity information during the preparation of the specimen. Scale bars, a–c, 100 nm; d and e, 5 nm.
	FIGURE 13. Cryo-electron tomogram of an A-tubule→Ribbon→Protofilament transition, following extended thermal fractionation. a, a′, b, and b′, A-tubule (A) (a and a′) has disassembled into a protruding Ribbon (R) (b and b′) of four PFs with accompanying partition-associated material (pam, bracket); tomographic slices (labeled and unlabeled) show cross-sectional views. Because the structural markers necessary to orient the A-tubule (e.g. MIP2 and the B-tubule hook, see Fig. 7) have been lost, the polarity of the A-tubule is ambiguous, and thus only a range of PFs is given for the PFs that appear to be in contact with the partition-associated material. In the displayed orientation the A-tubule→Ribbon transition matches best to the structural appearance of the partition-associated material in an A-tubule viewed from the proximal/minus to distal/plus end, as displayed in Figs. 2 and 7, supplemental Movie S1, and Ref. 59. Note, however, that the partition-associated material appears to change its shape on the Ribbon (b and b′) compared with that in the intact A-tubule (a and a′), preventing an unambiguous polarity determination. c, d, e, and c′, longitudinal views of the same A-tubule→Ribbon transition shown in a–b′; the tomogram of the A-tubule was sliced along the planes indicated by red lines in a. Black arrowheads in a–c point to the same PF, continuous through the bend/break in the Ribbon (c). The successive longitudinal slices (c–e) show the Ribbon (R) protruding from the A-tubule (A) (c) but absent in slices below this level (d and e). c′, high magnification view of the termination of the Ribbon, with the two peripheral PF (white arrowheads) ending first, and eventually a single most stable filament (black arrowhead), which corresponds to the continuous PF in the bend/break (c), extending the furthest. It is not yet known whether this last, most stable PF is a tubulin protofilament or a tektin filament. Scale bars, a, a′, b, and b′, 10 nm; c–e, 20 nm; c′, 20 nm.

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