Figure 4. Dynein’s phi particle conformation and its potential coevolution with LIS1 function.

(A) A cartoon model for the dynein phi particle (green and aquamarine, heavy chains with AAA domains numbered; gray, accessory chains), with the four intermolecular contact points identified by cryoEM indicated. Bottom panel illustrates the steric clash (indicated by jagged yellow line) between a dynein-bound LIS1/Pac1 monomer (red, bound to the dynein motor domain in green), and the 2^nd motor domain (in aquamarine; adapted from Marzo et al., 2020). (B) High resolution cryoEM structures of the four intermolecular contact points that stabilize the human dynein phi particle (adapted from Zhang et al., 2017). Note that regions ii, iii and iv have been experimentally validated, while region i has not yet been tested for its contribution to phi particle assembly (Marzo et al., 2020; Zhang et al., 2017). (C) Phylogenetic tree of cytoplasmic dynein heavy chains from the indicated species, and summary of the degree of their conservation (or lack thereof) for the three validated intermolecular contact points that stabilize the phi particle (only those sequences annotated as cytoplasmic dynein-1 homologs were selected for this analysis; see Figure 4—figure supplement 1 for sequence alignments of all four regions; *note that the dynein heavy chain from Ustilago maydis is encoded by two separate genes, dyn1 and dyn2, which encode approximately 2/3^rd and 1/3^rd of the motor, respectively [Straube et al., 2001]). The residues listed above (for the human dynein heavy chain) are color coded according to their chemical properties, with their mode of interaction depicted in the cartoons (blue, positively charged residues, ‘+”; red, negatively charged residues, ‘-‘; yellow, hydrophobic residues, ‘Φ”). Degree of conservation for each residue is indicated as ‘Y’ (green, yes, conserved), ‘N’ (red, not conserved), or with a +/- value (yellow) indicating a potentially conserved residue up to three positions N- or C-terminally situated, respectively. ‘His’ indicates the presence of a histidine in these respective positions, which has the potential to form a salt bridge depending on the local microenvironment. The column on the right indicates whether a clear LIS1 ortholog was identified by sequence alignment or genome annotation (‘Y’, homolog present). Species names indicated in red are those in which no LIS1 homolog was identified. Note that the five species with no apparent LIS1 homolog exhibit a low predicted propensity to adopt the phi particle, as determined by the sequence alignments.

Figure 4—figure supplement 1. Sequence alignments of the intermolecular contact regions for cytoplasmic dyneins from disparate species.

Alignments of the four predicted intermolecular contact points that stabilize the phi particle conformation (listed in order from surfaces 1 through 4, as indicated). Cytoplasmic dynein-1 heavy chain sequences were identified based on sequence annotations. The numbered residues above each line (with *) denote the residues that mediate the intermolecular interactions (red and cyan depict residues experimentally validated, and those not yet tested, respectively; those in red were used to generate the table shown in Figure 4C). See Figure 4B for precise predictions of interacting residues. For each starred residue, a conserved residue in each ortholog is denoted in green, and potentially conserved residues (offset by up to three positions in the N- or C-terminal direction) are denoted in yellow. If no potentially conserved residue was identified, the residue is denoted in black. Species names in red indicate those species with no apparent LIS1 homolog.