Panel Showing the Protein-Based Phylogenies of the Cytoplasmic Dynein Subunit Families

<div><p>Species names are shown with NCBI/GenBank gene/protein names. NCBI/GenBank protein-sequence accession numbers are given in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020001#pgen-0020001-st001" target="_blank">Table S1</a>. Orthologous human, mouse, and rat gene names use the revised systematized consensus nomenclature (e.g. DYNC1H1 in humans, mouse, and rat). Relationships amongst dynein sequences of different species do <i>not</i> necessarily reflect the evolutionary relationships amongst species; see [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020001#pgen-0020001-b208" target="_blank">208</a>] and [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020001#pgen-0020001-b209" target="_blank">209</a>] for further details. Named clades are indicated in the right margins. Bayesian and maximum-likelihood bootstrap values are shown as percentages (top and bottom, respectively), adjacent to branch points. Asterisks denote bootstraps below 50%. Filled circles denote bootstraps at 100%. Scale-bar represents evolutionary distance (estimated numbers of amino-acid substitutions per site).</p><p>(A) Cytoplasmic dynein heavy chain family. <i>Chlamydomonas</i> outer arm heavy chain <i>(ODA11)</i> is used as the outgroup. DNAH12frag is the partial axonemal heavy chain fragment taken from [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020001#pgen-0020001-b023" target="_blank">23</a>]. For mouse DYNC2H1, XP_35830, only partial protein sequence (336aa) was available in the GenBank database. Adding this partial sequence to our analysis resulted in spurious clustering, therefore we obtained an extended, putative sequence by using BLAST (TBLASTN) against the mouse genome (Build 32) with human and rat sequences XP_370652 and NP_075413, respectively. Incomplete mouse genomic assembly at the <i>DYNC2H1</i> locus yielded a truncated sequence 3455 amino acids in length, 85% the length of human DYNC2H1.</p><p>(B) Cytoplasmic dynein intermediate chain family. The <i>Chlamydomonas</i> IC2 <i>(ODA6)</i> is used as the outgroup.</p><p>(C) Cytoplasmic dynein light intermediate chain family. There does not appear to be a sufficiently distant homolog in <i>Chlamydomonas</i> to be used as an outgroup in this analysis, therefore ODA11 (Q39610, a heavy chain protein) was chosen as the outgroup for this tree.</p><p>(D) Cytoplasmic dynein light chain Tctex1 family. The <i>Chlamydomonas</i> LC2 light chain is used as the outgroup.</p><p>(E) Cytoplasmic dynein light chain Roadblock family. The <i>Chlamydomonas</i> outer arm dynein LC7a, is used as the outgroup.</p><p>(F) Cytoplasmic dynein light chain LC8 family. The <i>Chlamydomonas</i> Q39579 sequence is used as an outgroup. This phylogeny is poorly resolved, with low bootstrap support values and posterior clade probabilities, most likely due to there being little variation amongst the ingroup sequences. We found good support for the LC8 light chain 1 clade, and some support for the LC8 light chain 2 clade, of four vertebrate sequences. The relationships of the two sequences, C. elegans and <i>Takifugu</i> were poorly resolved, and therefore we have not included these in the LC8 light chain 2 clade.</p></div

The Mammalian Cytoplasmic Dynein Complexes

<div><p>(A) Cytoplasmic dynein. (Left panel) Polypeptides of immunoaffinity-purified rat brain cytoplasmic dynein. Polypeptide mass (in kDa) is indicated on the right side of the gel, and the consensus family names are indicated on the left. (Right panel) Structural model for the association of the cytoplasmic dynein complex subunits. The core of the cytoplasmic dynein complex is made of two DYNC1H1 heavy chains which homodimerize via regions in their N-termini. The motor domains are at the C-termini of the heavy chains, the large globular heads of ~350 kDa that are composed of a ring of seven densities surrounding a central cavity; six of the densities are AAA domains (numbered 1–6). AAA domain 1 is the site of ATP hydrolysis. The microtubule-binding domain is a projection found on the opposite side of the ring between AAA domains 4 and 5. C is the C-terminus of the heavy chain that would form the 7th density. Two DYNC1I intermediate chains (IC74) and DYNC1LI light intermediate chains bind at overlapping regions of the N-terminus of the heavy chain, overlapping with the heavy chain dimerization domains. Dimers of the three light chain families; DYNLT, the Tctex1 light chains; DYNLRB, the Roadblock light chains; and DYNLL, the LC8 light chains, bind to the intermediate chain dimers.</p><p>(B) Cytoplasmic dynein 2 complex, structural model for subunit association. This dynein complex has a unique role in IFT and is sometimes known as IFT dynein. Structural predictions indicate that the heavy chain, DYNC2H1, is similar to the cytoplasmic and axonemal dyneins. The only known subunit of this complex is a 33- to 47-kDa polypeptide, DYNC2LI1, which is related to the cytoplasmic dynein light intermediate chains. No intermediate chain or light chains have yet been identified [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020001#pgen-0020001-b016" target="_blank">16</a>].</p></div