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Three distinct inner dynein arms in Chlamydomonas flagella: molecular composition and location in the axoneme.

The molecular composition and organization of the row of axonemal inner dynein arms were investigated by biochemical and electron microscopic analyses of Chlamydomonas wild-type and mutant axonemes. Three inner arm structures could be distinguished on the basis of their molecular composition and position in the axoneme as determined by analysis of pf30 and pf23 mutants. The three inner arm structures repeat every 96 nm and are referred to here as inner arms I1, I2, and I3. I1 is proximal to the radial spoke S1, whereas I2 and I3 are distal to spokes S1 and S2, respectively. The mutant pf30 lacks I1 whereas the mutant pf23 lacks both I1 and I2 but has a normal inner arm I3. Each of the six heavy chains that was identified as an inner dynein arm subunit has a site for ATP binding and hydrolysis. Two of the heavy chains together with a polypeptide of 140,000 molecular weight form the inner arm I1 and were extracted from the axoneme as a complex that had a sedimentation coefficient close to 21S at high ionic strength. Different subsets of two of the remaining four heavy chains form the inner arms I2 and I3. These arms at high ionic strength are dissociated as 11S particles that include one heavy chain, one intermediate chain, two light chains, and actin. These and other lines of evidence indicate that the inner arm I1 is different in structure and function from the inner arms I2 and I3.

Abstract. The molecular composition and organization of the row of axonemal inner dynein arms were investigated by biochemical and electron microscopic analyses of Chlamydomonas wild-type and mutant axonemes. Three inner arm structures could be distinguished on the basis of their molecular composition and position in the axoneme as determined by analysis of pf30 and pf23 mutants. The three inner arm structures repeat every 96 nm and are referred to here as inner arms I1, 12, and 13. I1 is proximal to the radial spoke S1, whereas 12 and 13 are distal to spokes S1 and $2, respectively. The mutant pf30 lacks I1 whereas the mutant pf23 lacks both I1 and 12 but has a normal inner arm 13. Each of the six heavy chains that was identified as an inner dynein arm subunit has a site for ATP binding and hydrolysis. Two of the heavy chains together with a polypeptide of 140,000 molecular weight form the inner arm I1 and were extracted from the axoneme as a complex that had a sedimentation coefficient close to 21S at high ionic strength. Different subsets of two of the remaining four heavy chains form the inner arms 12 and I3. These arms at high ionic strength are dissociated as l lS particles that include one heavy chain, one intermediate chain, two light chains, and actin. These and other lines of evidence indicate that the inner arm I1 is different in structure and function from the inner arms 12 and 13.
T HE inner dynein arms, unlike the outer dynein arms, are both necessary and sufficient to generate ciliary and flagellar axonemal bending (4). However, the molecular organization and composition of the inner dynein arms are not as well understood as those of the outer row of arms (for review see references 8, 16, 17, and 25). Through biochemical and electron microscopic analyses of Chlamydomonas wild-type and mutant axonemes, here we have begun to determine the composition of each inner dynein arm. In addition, we demonstrate that the row of inner arms is formed by three distinct structures, each having a specific location relative to the radial spokes S1 and $2 (see references 7 and 8).
Several lines of evidence have suggested that the row of inner dynein arms is formed by more than one type of structure. First, as many as five inner arm heavy chains were identified by combined biochemical and microscopic analysis of Chlamydomonas mutants lacking either outer or inner dynein arms (11). Therefore, the existence of multiple inner arms was implied, as all dynein arms characterized so far are formed by at most three heavy chain subunits (6,28). Second, in contrast to mutations affecting outer arm assembly, which cause the loss of all outer arm heavy chains along with the outer arms (15), mutations known to affect the assembly of inner arms cause the lack of only a subset of inner arm heavy chains (4,20). Third, EM of quick-frozen and deepetched samples has revealed that there are two types of inner arm structures, referred to as dyads and triads organized in triad-dyad-dyad triplet groups which repeat with a 96-nm interval (7,8). Together, these data suggest that the inner dynein arms, unlike the outer dynein arms, are heterogeneous in structure and composition.
To further investigate this hypothesis of inner dynein arm organization, we have adopted new electrophoretic conditions for separation of inner arm heavy chains and then reexamined inner ann deficient mutants described previously (4,11,20). We have also analyzed those same mutants by EM of longitudinal sections. Through these combined analyses we have determined the location of three specific types of inner arms in the axoneme and begun to investigate their function.

Strains and Culture of Chlamydomonas Cells
The strain 137c, mating type +, was adopted as wild type. The mutants analyzed in this study are listed in Table I. recombinant strains pf30pf28, pf14pf28, and pflgpf28 were selected from nonparental ditype tetrads, whereas pf23pf28 was selected from a tetratype tetrad. Cells from each recombinant strain have short (approximately half of the normal length or less), paralyzed flagella. 4-d cultures and 35S-labeling of cells were performed on solid medium containing 25 mCi/liter of 135S]sulfuric acid (18). Determination of protein concentrations and radioactivity were as described (21). For certain electron microscopic experiments, flagella were isolated by the dibucaine method (29). Flagella prepared by the dibucaine or the pH shock method appeared identical in structure and composition.

Electrophoresis and Densitometry of Autoradiograms
Electrophoresis of dynein heavy chains was performed essentially as described by Piperno (20). However, the following modifications were introduced to improve the resolution of inner dynein arm heavy chains. We used a discontinuous slab gel composed of a 3.2 % polyacrylamide stacking layer and a 3.6-5 % polyacrylamide resolving layer. The slab did not contain urea. Ultra pure acrylamide from International Biotechnologies, Inc. (New Haven, CT) and sodium dodecyl sulfate 99.0% pure from BDH Laboratories (Poole, UK) were used for the preparation of gels. These new conditions led to the resolution of six electrophoretic bands each containing at least one inner dynein arm heavy chain from pf2g axonemes ( Fig. 1). In contrast, polypeptides I, II, and V of wild-type axonemes, the ~x, B, and 3, heavy chains, respectively of outer dynein arms (22) were not resolved from each other and from polypeptides III and IV of the inner dynein arms. Instead they formed two electrophoretic bands (Fig. 1, first lane [also see Fig. 1, reference 20). Under these new electrophoretic conditions, polypeptides I, II, and HI compose the slowest major band, whereas polypeptides IV and V compose the second major band. The electrophoretic mobilities of these components were determined by comparing the electrophoretic patterns formed by axonemal polypeptides of the mu-tantspf28, pf30, and the recombinant strainpf28pf30, pf28 and pf30 lack polypeptides I, II, and V, and HI and IV, respectively (20). Therefore, using the new conditions of gel electrophoresis it was possible to identify polypeptides HI and IV as defined under the previous conditions of gel electrophoresis. In contrast, it was not possible to identify which of the remaining four bands, formed by pf28 inner arm heavy chains under the new conditions of electrophoresis, corresponded to inner arm electrophoretic components VI, and VII, and VIII as defined previously (11,24). Densitometry of autoradiograms was performed with a video densitometer (model 620; Bio-Rad Laboratories, Richmond, CA). Quantitative measurements were performed in the range of linear response of autorndiogmms of gels produced by exposure for an appropriate length of time. 1D Analyst Software (Bio-Rad Laboratories) was used to determine relative optical density of each electrophoretic band.

Electron Microscopy
For structural study, isolated axonemes were sedimented at 10,000 g, and pellets were fixed with 1% glutaraldehyde and 1% tannic acid in a buffer containing sodium cacodylate as described previously (11). Specimens were postfixed in osmium tetroxide, dehydrated in a graded series of ethanol, and embedded in Medcast-Araldite resin (Ted Pella, Inc., Tnstin, CA). 40-50 nm-thick uniform silver-gray sections were mounted on formvar coated, carbon stabilized copper grids, stained with uranyl acetate and Reynolds lead citrate, and examined at 80 kV in the JEOL 100 CX electron microscope (JEOL USA, Peabody, MA). Transverse and longitudinal sections of axonemes of wild-type and mutant cells were randomly selected and compared from more than one experiment for each cell type.

Nomenclature
New information concerning the organization of the row of inner dynein arms and the molecular composition of each arm is reported in the following section. On the basis of these data, we have adopted a new nomenclature to indicate each inner dynein arm and each heavy chain subunit that we have identified. This nomenclature reflects our present understanding of the inner dynein arm structures. However, it is not yet definitive because we have limited information on differences of primary structures and/or modifications existing among the inner dynein arm heavy chains.
Three distinct inner dynein ann structures are referred to as 11, 12, and I3, in the order of their position relative to the radial spokes. The inner arms I1 and I2 are proximal to the radial spoke $1 and $2, respectively, whereas I3 is distal to $2.
The denomination of each inner dynein heavy chain includes a number and a Greek letter or a prime. The number refers to the inner arm that contains the heavy chains. The Greek letters refer to polypeptides that are associated in 1:1 ratio, are not labeled by 32p in vivo (24) and may differ in their primary structure. The prime refers to polypeptides that form a minor satellite band in motile and long flagella. Thus, as described below, the inner dynein ann I1 is formed by the heavy chains h~ and 1/3, whereas the inner arms 12 and 13 are formed by the heavy chains 2' and 2 and 3 and 3', respectively. The inner arm heavy chains 1~ and 1/~ are the polypoptides formerly indicated as components HI and IV (22). The heavy chains 2; 2, 3, and 3' formed the components formerly indicated as VI, VII, and VIII, which were found to be phosphorylated in vivo (24).
Until specific reagents are developed (e.g., monospecific antibodies) to identify each inner arm heavy chain, it will be necessary to use axonemes from the recombinant strains pf30pf28 and pf23pf28 as standards for the electrophoretic analysis of inner arm heavy chains. It will be shown in the following section that the recombinant strains pf30pf28 and pf23pf28 lack the dynein arm heavy chains forming the inner arm I1 and I1 and 12, respectively, as well as the outer dynein arms.

Molecular Composition and Heterogeneity of Inner Dynein Arms
We began our analysis of the molecular composition of the inner dynein arms, and putative heterogeneity of those components, by focusing on the resolution of dynein heavy chain subunits of the motile outer dynein-less mutant pf28 (19).
We resolved inner arm heavy chains o f p f 2 8 axonemes into six electrophoretic bands using the new electrophoretic con-ditions described in Materials and Methods (Fig. 1, second lane). Under the same conditions outer and inner dynein arm heavy chains of wild-type axonemes are resolved into six electrophoretic bands instead of eight, as illustrated in Fig.   1 (first lane). In pf28, the upper two bands have approximately the same intensity, whereas the lower four bands differ in intensity. The patterns of the four lower bands are identical in both lanes, therefore they may be formed uniquely by inner arm heavy chains.
Additional lines of evidence as described below confirm that the six bands shown in Fig. 1 (second lane) were formed by the inner arm heavy chains. First, these polypeptides were extracted in the presence of 0.5 M NaCI, ATE and Mg 2÷. Second, each of the six polypeptides was isolated or partially purified in association with intermediate and light chains that had previously been identified as inner dynein arm components (11,20,24). Finally, the same six polypeptides were specifically photocleaved by UV irradiation in the presence of ATE Mg 2÷, and vanadate (6).
Salt extracts from pf28 axonemes were prepared and aliquots were irradiated at 365 nm as described in Materials and Methods. Samples from untreated and irradiated extracts were then sedimented in a 5-20% sucrose gradient  Each polypeptide subunit is identified by its apparerlt molecular weight x 10 -~ with the exception of the actin. An estimate of the molecular weight of each heavy chain was obtained by adding the molecular weight values of their putative photocleavage products. * Differences in the composition of 1 IS complexes were detected by the analysis of fast and slow sides of the 1 IS peak. As in Fig. 3 A, each heavy chain, which appeared to be photocleaved, is indicated by a different symbol (open and closed circles, squares, and triangles).
containing 0.5 M NaC1. Profiles of sedimentation peaks obtained with an untreated extract are shown in Fig. 2 A. A major and minor peak with sedimentation coefficients of ~11S and 21S were resolved. Components of the irradiated salt extract sedimented like those of the untreated extract (not shown).
The polypeptide components of fractions 9-26 were then resolved by electrophoresis (Fig. 2 B). The minor 21S peak is formed by dynein heavy chains and a polypeptide of 140,000 molecular weight. The major llS peak is formed by dynein heavy chains, a polypeptide of 133,000 molecular weight, actin and two light chains of 28,000 and 19,000 molecular weight. The distribution of the intermediate and light chains in the 11S peaks is asymmetric: the 133,000 and 19,000 components are enriched in the faster and slower regions of the peak, respectively. A summary of the polypeptides forming the two sedimentation peaks is reported in Table II. On the basis of their apparent molecular weights and with the exception of the 133,000 component, each of these polypeptides is identical to inner arm subunits described in previous studies (reviewed in reference 17). Two polypeptides with molecular weight 155,000 and 131,000 sediment between the l lS and 21S peaks. They may derive from the 21S complex and be dissociated during sedimentation. The ot and/~ tubulin subunits are present in each fraction as a contaminant.
The heavy chain components of peak fractions 14, 20, and 22 were further resolved by electrophoresis in low percentage gels as described above (Fig. 3 A). The 21S peak, fraction 14, contains two high molecular weight polypeptides, whereas the llS peak, fraction 20 and 22, contains three or four polypeptides which are partially resolved (lines and symbols, Fig. 3 A). The 21S heavy chains are characterized by lower mobility and equal intensity, whereas the llS heavy chains have higher mobilities and differ in intensity. These results suggest that the 21S component is a complex containing equal amounts of two inner arm heavy chains and the 11S peak is a heterogeneous mixture of inner dynein arm subunits.
As mentioned above, the six polypeptides indicated in Fig.   3 A were identified as dynein heavy chains also on the basis of their sensitivity to UV-induced photocleavage performed in the presence of ATP, Mg 2+, and vanadate. Nonirradiated and irradiated salt extracts were sedimented through identical sucrose gradients. Photocleavage was detected by comparing autoradiograms of gels in which equal amounts of radioactivity were analyzed from fractions 14, 20, and 22 from those sucrose gradients, Fig. 3 A. The asterisks distinguish those samples containing polypeptides that were subjected to photocleavage. Each of the six electrophoretic bands was reduced in intensity after photocleavage although the reduction was not uniform for each component. The occurrence of different extents of photocleavage for each of the six components under investigation is also shown by the electrophoretograms of cleavage products, which are present in fractions 14", 20 °, and 22 °, Fig. 3 B. The relative amount of each cleavage product in those fractions can be estimated because the 35S uniformly labels each heavy chain. In fact, the levels of intensity of heavy chains and cleavage products in the autoradiograms are similar to those that are revealed by silver staining in the gels (not shown).
We tentatively identified the fragments generated from each heavy chain by comparison of the intensity of heavy chain bands with intensities and distributions of cleavage products. For example, the first heavy chain characterized by the lowest electrophoretic mobility is cleaved less than the second heavy chain (Figs. 3 A, lanes 14 and 14"). Therefore, it may generate the two fragments that form bands of lower intensity (Fig. 3 B, lanes 14 and 14*, indicated by closed circles). The same logic, based on the evaluation of band intensity, was followed to match five additional sets of heavy chain precursor and cleavage products. A different symbol was adopted for each set of heavy chain and cleavage fragments (Fig. 3, A  Each heavy chain produced a large fragment of ,x, 250,000 molecular weight and the fifth and sixth heavy chains apparently generated two large fragments that were not resolved by electrophoresis (Fig. 3 B, fractions 20* and 22', open and closed triangles). The fifth and sixth heavy chains, as described below, also appeared to be interconvertible by posttranslational modification.
The apparent molecular weight of each of the six heavy chains was calculated by adding the molecular weight of their putative products of photocleavage. These molecular weights are reported in Table 1I. They are indicated with the corresponding symbols that distinguish each heavy chain, which appeared to be photocleaved.
The evidence described thus far suggests the existence of six heavy chains which compose the inner row of dynein arms. The evidence also suggests that there are at least two forms of inner arms; one form composed of the two heavy chains sedimenting as a 21S complex, the other form or forms composed of the remaining four heavy chains. These four polypeptides either have different primary structures and derive from separate subsets of inner dynein arms or have the same primary structures and derive from identical inner arms. In this case, they are resolved by gel electrophoresis because they are modified posttranslationally. To further investigate these points we analyzed other outer and inner dynein defective mutants.

Inner Arm Heavy Chains of Motile and lmmotile and Short Flagella
The relative intensity of a subset of the electrophoretic bands formed by the inner arm heavy chains changes depending on whether they are derived from axonemes of motile or immotile and short flagella. The outer arm-less mutantpfl3A has immotile, short flagella in contrast to the outer arm-less mutants pf28, odal, and oda6, which have motile flagella (15). Quantitative densitometry of electrophoretograms indicates that the sum intensity of the lower three bands ofpf 13A is very close to that of the four lower bands in pf28, odal, and oda6 after normalization toward the upper two bands (data not shown). Therefore, a form of posttranslational modification may result in changes of mobility of heavy chain polypeptides. These changes may be related to the motility and/or the length of the flagella under analysis. Alternatively, a subset of inner arm heavy chains including those forming the two upper bands and two lower bands is absent in immotile and short flagella.
To further test these hypotheses we analyzed flagella and axonemes of the recombinant strains pf14pf28 and pflS-pf28, because mutations at the PF14 or PF18 locus are correlated with drastic reduction of flagellar movement. In addition the recombinant pf14pf28 and pflSpf28 have short flagella. The electrophoretograms of the heavy chains of the recombinants (Fig. 5) are very similar to that of the mutant pfl3A (Fig. 4). Therefore, the relative intensity of the three lower bands formed by inner ann heavy chains changes in correlation with the motility and the length of the flagella under investigation. Furthermore, these experiments show that the five heavy chains ofpfl3A and the recombinant strains are indeed derived from inner dynein arms, and are not located in the radial spokes or central complex of the axoneme because pf 14 and pf 18 axonemes lack the radial spokes and the central complex, respectively. The results of these experiments suggest that a subset of the six inner arm heavy chains is differentially modified or absent in motile or immotile and short flagella. Additional data from other immotile and short inner arm mutants (discussed below) are also consistent with these results. However, these results do not resolve the issue of whether the 11S heavy chains form one or two kinds of inner dynein arms of distinct location within the axoneme. To address this question, we used electrophoretic and electron microscopic analyses of inner arm components in inner arm defective mutants.

Inner Arm Mutants Lacking Different Subsets of Heavy Chains
The investigation concerned with the heterogeneity of the inner dynein arms was continued with the analysis of the mutants pf23 and pf30 because previous studies had revealed that these mutants are partially defective for inner arm structures and inner arm heavy chains (4,11,20).
The mutants pf30 and pf23 have normal outer dynein arms. Therefore, we isolated and analyzed recombinant strains pf30pf28 andpf23pf28 to eliminate the interference of outer arm heavy chains in the electrophoretic resolution  of inner arm heavy chains. We analyzed recombinant strains pf30pf28 and pf23pf28, which both have immotile and short flagella, by electrophoresis and compared them with the immotile and short outer arm-less mutantpf 13A (Fig. 6). The mutantspf30 andpf23 were included as additional standards. These mutants have motile and normal in length flagella and immotile and short flagella, respectively. Flagella, instead of axonemes, were adopted for the analysis to avoid potential losses of dynein arms during the isolation.
Electrophoretic patterns formed by inner arm heavy chains

Electron Microscopy in Mutants Lacking Different Subsets of Inner Arm Heavy Chains
The existence of three distinct inner arm structures was confirmed by EM of longitudinal sections of axonemes from the mutants pf30 and pf23. Two section planes, A and B as illustrated in F!g. 7, were chosen for analysis. Section A bisects the axoneme since most or all of the central complex is seen (Fig. 8, left). The S1 and $2 radial spokes are viewed in their entirety in such sections. Section B is a glancing section that does not include the central complex and in which the radial spokes are viewed in cross section or end on (Fig.   8, right). In both section types the proximally directed tilt of the outer arms (10) is seen in wild-type, pf30, andpf23 axonemes and permitted determination of the orientation of the axoneme: the proximal end is to the left in Fig. 8. Interpretative tracings are included beneath each micrograph. Both A and B sections of wild-type axonemes show the row of inner dynein arms as a nearly continuous ribbon of electron opaque material but occasionally interrupted by indentations or small spaces, indicaied by vertical lines and arrows in Fig. 8, that repeat between spoke group pairs with a 96-nm period. The indentation or space between groups of inner arms appears to be the same defined in other structural studies using quick freeze and rotary shadow methods (for discussion see reference 8). The inner row of dynein arms is thus likely to be formed by groups of structures repeating with the same periodicity as the paired spokes (7,8). Additional microscopic images ofpfl4pf28 and pf18pf28 confinned that the inner row of dynein arms is formed by groups of structures delineated by indentations of specific location between spoke group pairs repeating every 96 nm (data not shown). Therefore, the lack of radial spokes or central components or outer dynein arms does not affect the grouping of inner arm structures resolved by thin sections.
In contrast to axonemes with complete sets of inner dynein heavy chains, similar longitudinal sections ofpf30 andpf23 revealed the existence of obvious and relatively large gaps in the row of inner dynein arms, indicated by arrowheads in Fig. 8. In all cases, gaps and intervening stained inner arms have a repeat of 96 nm in constant position and polarity relative to radial spoke organization. The gaps seen in pf30 are located in the large interval defined by the radial spokes just proximal to spoke S1, the proximal spoke of each pair, and  comprise approximately one-third the length of the 96 nm repeat (37 + 8 nm, n = 30: for criteria used to measure gaps see legend to Fig. 8). Gaps of the same size (37 + 8 nm, n = 30) and location were also seen in sections of the recombinant mutant pf30pf28, indicating that the lack of outer arms does not affect the spacing of the inner arms. Moreover, in an independent study of pf30 using quick-freeze, rotary shadow replication, a gap was also found just proximal to each radial spoke S1 (Goodenough, U. W., personal communication).
Occasionally gaps of similar size and disposition as in pf30 axonemes were found in wild-type axonemes (Fig. 8,  top right, indicated by arrow). In order to evaluate the significance of that morphological variation we determined gap frequency for 34 consecutive spoke group repeats >3.0/~m of randomly selected, longitudinally sectioned axonemes from wild-type and pf30. Four gaps, •25 um wide, were identified in wild-type axonemes. In contrast 28 gaps, ~35 nm wide, were identified in pf30. Therefore, the origin of the gaps observed in wild-type axonemes is different from that of the gaps found in pf30 axonemes. Regular repeating gaps were also found in pf23 inner arms. These gaps were much larger spanning about twothirds of the 96-nm spoke repeat interval (67.9 + 5 nm, n = 31) and encompassed the gap found inpf30. In an analysis similar to that described above, 30 gaps, *65 nm wide, were found in 34 consecutive spoke repeats >3.0/~m of randomly selected axonemes from pf23 ceils. The remaining inner arm structure of pf23 axonemes was found under and just distal to $2. These combined structural and biochemical analyses of inner arm defective mutants indicate that a pair of inner arm heavy chains, let and lfl, is missing in pf30 and correlate this deficiency with the gap making up approximately onethird of the 96-nm arm repeat. Four heavy chains, let, lfl, 2', and 2, are missing in pf23 and this correlates with a gap about two-thirds the length of the 96-nm repeat. These results are consistent with a model in which components let and 1/~ form an inner arm located proximal to spoke S1, referred to as inner arm I1, and components 2' and 2 form an inner arm structure located proximal to $2, referred to as 12. Therefore, a third inner arm, I3, located at the base and distal of the spoke $2 would be composed of heavy chains 3 and 3'.

The Organization of the Row of the Inner Dynein Arms
The evidence described in the preceding section has revealed the following aspects of the molecular composition and the organization of the inner dynein arms row. First, the inner arms can be distinguished as three different structures that are located in precise positions relative to the radial spokes. Second, each inner arm structure is composed of two heavy chains each having a site for ATP hydrolysis. Finally, the inner arms 12 and 13 were found to be more similar to each other than to the inner arm I1. These new insights were obtained by an electrophoretic procedure resolving the inner arm heavy chains into six components and by electron microscopy of longitudinal sections of wild-type and mutant axonemes. In addition, recombinant strains carrying the pf28 mutation (lacking the outer dynein arms) were con-structed and analyzed whenever outer arm heavy chains interfered with the resolution of inner ann heavy chains.
On the basis of this new evidence, the row of inner dynein arms appears to be formed by three distinct inner arms that are organized in groups of three and repeat at 96 nm. This model is in agreement with the models of inner dynein arm organization proposed by Goodenough and Heuser (7,9) which were derived from quick-freeze, rotary shadow, structural analyses of unfixed axonemes. Goodenough and Heuser described two morphologically distinct inner arm types: one termed a triad and the other termed a dyad. The triads and dyads alternate every 96 nm along each doublet microtubule in sets formed by one triad and two dyads. Based upon the position relative to the spokes we conclude that I1 is identical to what was termed a triad and 12 and 13 are the proximal and distal dyads, respectively. Our results are inconsistent with other models in which inner and outer rows of arms are thought to be identical in organization (2).
The triad (I1) was originally defined based upon the observation, in metal replicas, that it contained three large globular heads as opposed to the two heads in each dyad (7). To date, all dyneins have been shown to contain equal numbers of heavy chains and globular heads (28). Because the evidence described in this paper suggests that inner I1, the triad, is formed by two heavy chains, it would appear that the triad is an exception. However, the most recent description of inner arm images obtained by quick-freeze, deep-etch microscopy (8) redefine the triad as composed of a bilobed unit adjacent to a two-headed structure similar to a dyad. Therefore, a third globular domain of the triad, perhaps the bilobed structure, may not be composed of one of the inner arm heavy chains.
On the basis of our present understanding of the organization of the row of inner and outer dynein arms we can explain some results obtained in the past. Both mutants pf23 and pf30 were found to be defective for inner dynein arm structures by examination of cross-sectional images of isolated axonemes (4,11). We understand now that the absence or the reduction in intensity seen among the inner arm structures resulted from the lack of the inner arm I1 and 12 inpf23 and I1 inpf30. In fact, those defects were observed in cross sections of thickness close to the dimension of the periodic repeat of each inner dynein arm (for discussion see reference 4).
In the past, the resolution of outer and inner dynein arm heavy chains from Chlamydomonas wild-type and dynein arm defective mutants, suggested the existence of three outer and five inner dynein arm heavy chains that could be distinguished by the intensity of the electrophoretic bands formed by each of them (17). The bands of outer arm components were much more intense than those of inner arm components whereas components of each group were similar to each other. We presently know that within a 96-nm segment of outer doublet microtubules there are four outer dynein arms (9,11) and three inner dynein arms, respectively, composed of three and two heavy chains each. Therefore, the molar ratio of outer versus inner armheavy chains is 2:1 in agreement with what was observed earlier (11). Similarly, with respect to the inner arm heavy chain stoichiometry, Mitchell and Rosenbaum (19) describe four inner arm heavy chains in pf28 in an apparent ratio 1:1:2:2. Those data are consistent with our identification of six inner arm heavy chains.

Molecular Composition of Each Inner Arm
The following properties clearly distinguish the inner arm I1 from the inner arms I2 and 13. I1 is formed by at least three polypeptides that have distinctive electrophoretic mobility and are not dissociated upon sucrose gradient centrifugation at high ionic strength. In contrast, both 12 and 13 may be formed by the same group of light chains and are dissociated into 1 IS particles at high ionic strength. Further, I1 has a distinct "triad" structure compared to the dyad structure of 12 and 13 when studied in situ by the quick-freeze, rotary shadow method (8). Therefore, I1 is quite different from 12 and 13, and these last two are similar. We could distinguish between the inner arms 12 and 13 by analyzing the mutant pf23 and the recombinant strain pf23-pf28, because inner arm heavy chains 2' and 2 were lacking in the flagella of those strains in addition to the heavy chains let and 1/~. That deficiency could derive from the absence of the subunits composing the inner arm 12 or from the defect in a putative mechanism of posttranslational modification converting the heavy chain 3 into 2' and 2. However, this second event appeared unlikely because flagella of the strain pf23pf28 do not have a greater amount of heavy chain 3 than the flagella ofpf3Opf28, which have inner arm 12. Therefore, the heavy chains 3 and 2' and 2 are not in a precursorproduct relationship and the inner arm 12 is distinct from 13. The EM analyses confirmed this point. Posttranslational modifications converting the inner arm heavy chain 2 into heavy chain 2' and 3 into 3' may exist because the stoichiometry between the components of the two sets is altered in mutants carrying immotile and short flagella. Moreover, at least two of those heavy chains are phosphorylated in vivo (24). On this basis each of the inner arms 12 and I3 may be formed by two heavy chains that are identical in their amino acid sequence. On the other hand, there is no direct evidence that posttranslational modifications account for the differences in electrophoretic mobility of the heavy chains 2', 2, or 3, and 3'. Alternatively, the differences in the electrophoretic patterns of inner arm heavy chains that were observed when mutants with motile flagella were compared to mutants with immotile and short flagella could derive from a partial loss of components lot, 1~, 2, and 3'.
A form of actin is one of the light chains forming the inner arms 12 and I3 (23). In addition, the 19,000-molecular weight protein, cosedimenting with the actin in the 11S particles derived from I2 and I3, appeared to be identical to the calcium-binding protein caltractin which was initially identified as a Chlamydomonas basal body component (14).
Caltractin is also similar or identical to centrin (14,26). We have confirmed the identity of the 19,000 molecular weight protein and caltractin by electrophoresis and immunoblots of the polypeptides forming the 11S complexes from the inner arms. A polyclonal antibody to caltractin (14) (kindly provided by Dr. Bessie Huang, Research Institute of Scripps Clinic, La Jolla, CA) bound uniquely to the 19,000-molecular weight component (Piperno, G., unpublished observation). On this basis the inner arms I2 and I3 contain components that diZ.~rentiate them from I1 and may regulate their function.
A previous study showed that substoichiometric amounts of actin were found in llS fractions of 1~ and 1/~ heavy chains that were isolated by subsequent dialysis and sedi-mentation at low ionic strength (20). However, the association of actin with the I1 heavy chain may be adventitious in light of the observations described above and in the article of Goodenough et al. (9). The isolation of an actin-containing complex at low ionic strength, as was performed in the first study (20), probably was due to nonspecific binding of actin to the I1 heavy chains.

The Regulation of Motility by lnner Arm Components
The phenotypes of the mutants pf23 and pf30 indicate that the inner dynein arms regulate the movement of Chlamydomonas flagella in at least two ways depending on which inner arm is involved.
The lack of the inner arm heavy chains lu and 1~ in flagella of the mutant pf30 was correlated with a slight decrease of flagellar beat frequency and a remarkable change in flagellar bending pattern (4). On this basis the inner dynein arms were identified as structures influencing axonemal waveforms and microtubule sliding rate more than the beat frequency although only one specific inner dynein arm I1, was missing. The mutantpf23 was found to lack 'M5% of outer dynein arms and 86 % of inner dynein arms by examination of crosssectional images of isolated axoneme (11). We presently know that the mutant pf23 lacks the inner arms I1 and 12 but retains the inner arm I3 and most of outer dynein arms. Therefore as a result of our present analysis, the mutants pf23 and pf30 appear to differ mainly for the additional lack of inner arm 12 in the mutant pf23. This lack is correlated with the paralysis of pf23, although it does not involve a marked reduction in the number of outer and inner dynein arm heavy chains per unit length of the axoneme relative to that contained in pf30. Therefore, the defect of 12 apparently results in a greater inhibition of axonemal movement than would be predicted simply on the basis of the number of remaining dynein arms.
The possible involvement of the inner dynein arms 12 and 13 in a mechanism of regulation of axoneme motility is suggested by the following observations. The mutants lacking all or part of the radial spokes have nonmotile flagella, although they are normal in their outer and inner dynein arm structures (12). However, the same mutations in recombinant strains also carrying supps3 or sups4 or pf2 and pf3, allow for flagellar motility (13). The mutants pf2 and pf3 have the motility phenotype of inner arm-deficient mutants as does pf30 (4). In addition, they are deficient for the phosphorylation of at least one of the inner arm heavy chains forming the I2 and I3 structures (17). Therefore, that specific deficiency of the I2 and 13 inner arm heavy chains is correlated with the suppression of flagellar paralysis.
Additional lines of evidence implicate the inner arms 12 and 13 as structures involved in the regulation of flagellar motility. First, inner arm heavy chains, other than la and 1/~ lacking in pf30, are phosphorylated in vivo by pulse 32p_ labeling (24). Second, axonemal actin is a subunit of the complexes formed by 12 and I3 heavy chains. Finally, the 19,000-molecular weight protein cosedimenting with actin appears to be identical to the calcium-binding protein caltractin (14). Therefore, inner arms I2 and 13 display features that are involved in the regulation of other contractile sys-tems: actin, a calcium-binding protein, and the phosphorylation of subunits carrying ATPase activity.
In summary, we have identified some of the molecular components of the three inner dynein arms and revealed that the inner ann proximal to the S1 radial spoke, I1, is different in structure and function from the other two, 12 and 13, both located distal to a radial spoke. The inner arms I2 and I3 from their location in the axoneme may regulate both the radial spoke-central pair interactions (27) and the Ca 2÷dependent switching from a ciliary to a flagellar form of motion (3).