Cytoplasmic dyneins, the principal microtubule minus-end-directed motor proteins of the cell, are involved in many essential cellular processes. The major form of this enzyme is a complex of at least six protein subunits, and in mammals all but one of the subunits are encoded by at least two genes. Here we review current knowledge concerning the subunits, their interactions, and their functional roles as derived from biochemical and genetic analyses. We also carried out extensive database searches to look for new genes and to clarify anomalies in the databases. Our analysis documents evolutionary relationships among the dynein subunits of mammals and other model organisms, and sheds new light on the role of this diverse group of proteins, highlighting the existence of two cytoplasmic dynein complexes with distinct cellular roles.
Citation: Pfister KK, Shah PR, Hummerich H, Russ A, Cotton J, Annuar AA, et al. (2006) Genetic Analysis of the Cytoplasmic Dynein Subunit Families. PLoS Genet 2(1): e1. https://doi.org/10.1371/journal.pgen.0020001
Published: January 27, 2006
Copyright: © 2006 © 2006 Pfister et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Abbreviations: ATP, adenosine triphosphate; BBSRC, Biotechnology and Biological Sciences Research Council; IFT, intraflagellar transport; JTT, Jones, Taylor, and Thornton; MGI, Mouse Genome Informatics; Mr, relative mobility; NCBI, National Center for Biotechnology Information; NIH, National Institutes of Health; nNOS, neuronal nitric oxide synthase; PSI-BLAST, position-specific iterative BLAST; RefSeq, Reference Sequence
Dyneins are large multi-subunit protein complexes that undertake a wide range of roles within the cell. They are adenosine triphosphate (ATP)–driven, microtubule minus-end-directed molecular motors that can be divided, based on function, into two classes: axonemal and cytoplasmic dyneins [1–7] (reviewed in [8,9]). Axonemal dyneins are responsible for the movement of cilia and flagella. Two cytoplasmic dynein complexes have been identified. The most abundant cytoplasmic dynein complex, cytoplasmic dynein 1, is involved in functions as diverse as spindle-pole organization and nuclear migration during mitosis, the positioning and functioning of the endoplasmic reticulum, the Golgi apparatus, and the nucleus, and also the minus-end-directed transport of vesicles, including endosomes and lysosomes, along microtubules and retrograde axonal transport in neurons. A second cytoplasmic dynein complex, cytoplasmic dynein 2, has a role in intraflagellar transport (IFT), a process required for ciliary/flagellar assembly (reviewed in ).
The core of the cytoplasmic dynein 1 complex is a homodimer of two heavy chain polypeptides and associated intermediate, light intermediate, and light chain polypeptides, which are defined and named by their molecular mass and mobility in SDS-PAGE gels (Figure 1A). The protein subunits are encoded by families of at least two genes, and the expression patterns of the individual family members are different in various cell types. At least one of the light chains, DYNLL1 (LC8), has multiple cellular roles independent of its participation in a dynein complex. Cytoplasmic dynein 1 interacts with various other proteins including a second multimer, dynactin, to form the dynein–dynactin complex. Dynactin is comprised of at least seven different proteins, which together act as an adaptor that connects the cytoplasmic dynein motor to a range of cargoes (for review, see ). Interaction with dynactin also increases dynein motor processivity . Furthermore, dynactin functions independently of dynein, anchoring microtubules at the centrosome . Current evidence suggests that the second cytoplasmic dynein complex, cytoplasmic dynein 2, is also a homodimer of a distinct heavy chain, DYNC2H1, with associated light intermediate chain, DYNC2LI1 (Figure 1B). No other subunits have yet been identified for this complex, and it does not appear to interact with the dynactin complex [14–16].
(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.
(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 .
The cytoplasmic dynein proteins are fundamental to the functioning of all cells, and have recently been shown to be causally mutated in forms of neurodegeneration [17–19]. They are thus of great interest for mammalian genetic, and other, studies. We therefore sought to examine the role of cytoplasmic dynein subunits from a genetic perspective. During this analysis, we noted considerable confusion in the human and mouse gene and protein names and mapping positions. Therefore, we reexamined the mapping locations for the subunit genes and clarified and updated entries in the various sequence databases. In doing so, we utilized the revised consensus nomenclature developed for the cytoplasmic dynein subunits and their genes (Table 1). We also defined, as far as possible with current data, homologous genes in model organisms, including Drosophila, Caenorhabditis elegans, Chlamydomonas, and yeast. To further our understanding of the function of cytoplasmic dynein subunits, we also briefly examined mutations in this group of proteins in a variety of model organisms. We do not discuss dynein-binding proteins such as dynactin, LIS1, or various kinases, which while important for dynein function, have not yet been shown to be stoichiometric components of the cytoplasmic dynein complex.
Human and mouse cytoplasmic dynein subunit genes.
The subunits of the cytoplasmic dynein complexes are resolved into subunit polypeptides of ~530 kDa (heavy chains), ~74 kDa (intermediate chains), ~33–59 kDa (light intermediate chains), and ~10–14 kDa (light chains) in SDS-PAGE gels (Figure 1A). Research on the cytoplasmic dynein subunits has been undertaken in a wide range of organisms from yeast to humans. The nomenclature of the mammalian genes encoding these proteins has drawn on homologs in other organisms and, consequently, a number of aliases have been found for any given human or mouse cytoplasmic dynein subunit. Much of the early research into dynein genetics was conducted in the biflagellate green alga Chlamydomonas on the dyneins found in the flagellar axoneme, and therefore some cytoplasmic dynein nomenclature derives from these studies. For example, mammalian members of the cytoplasmic light chain families DYNLRB and DYNLL have commonly been referred to as LC7 and LC8, respectively, which are the names of homologous Chlamydomonas axonemal dynein subunits.
The revised classification system for mammalian cytoplasmic dynein (Table 1) recognizes the two distinct dynein complexes, cytoplasmic dynein 1 and cytoplasmic dynein 2, and the fact that cytoplasmic dynein light chains are shared with some axonemal dyneins. Cytoplasmic dynein subunits are also classified into polypeptide families according to sequence similarity within groups of similarly sized proteins; thus there is sequence similarity within the dynein gene families (and when cytoplasmic and axonemal members of the same gene families are compared) but not among them.
This nomenclature has been approved by the Human Genome Organization Nomenclature Committee  and the International Committee on Standardized Nomenclature for Mice. In accordance with their policy, the designation of each unique cytoplasmic dynein subunit starts with DYNC for dynein, cytoplasmic, followed by the specific dynein complex subtype 1 or 2; for example, cytoplasmic dynein 2 is designated DYNC2. The shared light chains start with DYN. Each subunit is designated with a letter(s) for the size of the polypeptides, H for the heavy chain, I for the intermediate chain, LI for the light intermediate chain, and L for the light chain. Additional letters (T, RB, and L) are used to distinguish the three distinct light chain families as described in the text. Individual members of the gene families are assigned numbers. Standard human and mouse gene nomenclature is used: italicized upper case for human gene symbols (for example, DYNC1H1), italicized initial upper case and then lower-case letters for mouse (Dync1h1), and for proteins of both species, the same symbols in upper case, upright (DYNC1H1). In accordance with the International Union of Pure and Applied Chemistry standards, isoforms of the intermediate chain gene products are referred to with letters. This nomenclature system can be expanded to other subunits as appropriate. We refer to mapping positions using the prefixes Hsa (Homo sapiens) for human and Mmu (Mus musculus) for mouse, followed by the chromosomal localization e.g. Hsa2q11, Mmu11.
Table 1 lists the aliases, map position, and protein/DNA-sequence accession data for each known mouse and human cytoplasmic dynein gene. The greatest number of aliases was observed for the cytoplasmic dynein 1 heavy chain 1 (DYNC1H1) for which we identified 15 different names. Some alternative cytoplasmic dynein gene names have come from large-scale gene and transcript identification efforts such as the partial DYNC1H1 clone KIAA0325 and its mouse homolog “mKIA00325,” generated by the Kazusa cDNA project . A small number of gene names have been derived from the names of DNA markers and cDNA clones used to identify the genes, for example, cytoplasmic dynein 2 light intermediate chain 1, DYNC2LI1, was named DKFZp564A033 after the cDNA sequence and clone of the same name. The heavy chain gene DYNC1H1 has also been referred to by the name of a marker, Hp22, generated from its human cDNA sequence, as well as the rat-derived marker Rk3–8 and a cDNA clone named HL-3.
Cytoplasmic Dynein Heavy Chain Gene Family (DYNC1H1, DYNC2H1)
Figure 2A shows the phylogenetic relationships amongst the dynein heavy chain protein sequences from various organisms. The heavy chain sequences fall into two distinct clades, and the relationships within each clade are generally consistent with known evolutionary distances between the organisms shown. We note that our phylogeny fits well with and extends previous phylogenetic analyses of the heavy chain proteins [22,23]. This analysis indicates that the partial human sequence DNAH12, (AAB09729) , is unlikely to be a cytoplasmic dynein.
Species names are shown with NCBI/GenBank gene/protein names. NCBI/GenBank protein-sequence accession numbers are given in Table S1. 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 not necessarily reflect the evolutionary relationships amongst species; see  and  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).
(A) Cytoplasmic dynein heavy chain family. Chlamydomonas outer arm heavy chain (ODA11) is used as the outgroup. DNAH12frag is the partial axonemal heavy chain fragment taken from . 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 DYNC2H1 locus yielded a truncated sequence 3455 amino acids in length, 85% the length of human DYNC2H1.
(B) Cytoplasmic dynein intermediate chain family. The Chlamydomonas IC2 (ODA6) is used as the outgroup.
(C) Cytoplasmic dynein light intermediate chain family. There does not appear to be a sufficiently distant homolog in Chlamydomonas to be used as an outgroup in this analysis, therefore ODA11 (Q39610, a heavy chain protein) was chosen as the outgroup for this tree.
(D) Cytoplasmic dynein light chain Tctex1 family. The Chlamydomonas LC2 light chain is used as the outgroup.
(E) Cytoplasmic dynein light chain Roadblock family. The Chlamydomonas outer arm dynein LC7a, is used as the outgroup.
(F) Cytoplasmic dynein light chain LC8 family. The Chlamydomonas 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 Takifugu were poorly resolved, and therefore we have not included these in the LC8 light chain 2 clade.
Cytoplasmic dynein heavy chain 1, DYNC1H1.
DYNC1H1, cytoplasmic dynein 1 heavy chain 1, is the largest cytoplasmic dynein subunit, having ~4,600 residues and a molecular weight of >530 kDa. First identified in rat spinal cord and brain and termed Microtubule Associated Protein 1C (MAP1C) , DYNC1H1 is a distant member of the AAA family of ATPases and is the cytoplasmic counterpart to axonemal dynein heavy chains [3,25]. DYNC1H1 associates as a homodimer within the cytoplasmic dynein complex and effects the contact and translocation of the dynein complex along microtubules via its large motor domain [8,26] (Figure 1B).
The C-terminal region of DYNC1H1 is the motor domain of the dynein complex and is conserved in all cytoplasmic and axonemal dynein heavy chains. This region is arranged as a heptameric ring with six AAA domains and a seventh domain, the identity of which remains a matter of discussion (Figure 1B) [12,25,27,28]. AAA domains are regions of ATP binding and hydrolysis, and thus they generate the energy required for translocation [29–31]. While the first AAA domain is essential for motor activity , reviewed in , the first four AAA domains are potentially capable of binding and hydrolysing ATP [33–35]. Contact of the heavy chain with a microtubule is established via an ~15-nm projection that extends between the fourth and fifth AAA domains [28,36]. The N-terminal region of DYNC1H1 is known as the stem, and force production, and therefore translocation, is thought to be achieved through the contact and shift of a 10-nm fold of the stem closest to the first AAA domain . DYNC1H1 dimerization also occurs in the stem, and the intermediate chains and light intermediate chains bind in this region as well [38,39]. The three light chains bind to the intermediate chains . Collectively the five smaller dynein subunits that bind to the N-terminus of DYNC1H1 make up the cargo-binding portion of the dynein complex.
The sequence of full-length mammalian DYNC1H1 was first obtained in rat and mouse [41,42]. Human DYNC1H1 was identified by screening an adenocarcinoma library with a partial human cDNA [23,43]. As yet, the only mutations reported in mammalian heavy chains have been in the mouse: the Loa and Cra1 strains have allelic point mutations in Dync1h1 that cause late-onset motor neuron degeneration in heterozygotes and neuronal apoptosis in homozygotes . The loss of both copies of Dync1h1 has been shown to be lethal during early embryonic development, with disorganization of the Golgi complex, improper distribution of endosomes and lysosomes, and defects in cell proliferation; no phenotype has yet been reported for heterozygote knock-out mice .
In Drosophila, the dynein heavy chain gene, Dhc64C, functions in oogenesis [45,46], oocyte differentiation , centrosome attachment during mitosis , eye development, cell development in thorax, abdomen, and wing , and axonal transport . Homozygous mutations induced by the mutagen ethyl methane sulfonate in Dhc64C are larval/pupal lethal, whilst heterozygotes have defects in bristle formation, eye development, and fertility . In C. elegans, dynein heavy chain (dhc-1) is an essential gene, also known as let-354 (LEThal) . Extensive mutational analysis has been conducted on dhc-1 to produce a range of variants from recessive/dominant lethals to temperature-sensitive mutants. The resultant phenotypes invariably include embryonic lethality, spindle orientation defects, polar body abnormalities, and excessive blebbing in the early embryo [51–54].
In the yeast Saccharomyces cerevisiae, heavy chain function ensures the alignment and orientation of mitotic spindles. Mutation of the S. cerevisiae heavy chain gene dyn1, which has 50% similarity (28% identity) to DYNC1H1 over 80% of the protein's length, has been shown to disrupt spindle orientation and reduce the fidelity of nuclear segregation during mitosis [55,56]. Despite this phenotype, dyn1 mutants remain viable, although dyn1 and kinesin double mutants are lethal . This observation suggests some functional redundancy for dynein by kinesin motors in yeast. No cytoplasmic dynein 1 heavy chain 1 homolog has unambiguously been identified in Chlamydomonas, and neither have dyneins been found in either the Arabidopsis or rice genomes [58,59] (reviewed in ). There are many dynein heavy chains in the Chlamydomonas genome. However, with the exception of DYNC2H1, they appear to be components of the axonemal dyneins.
Cytoplasmic dynein 2 heavy chain 1, DYNC2H1.
The cytoplasmic dynein 2 heavy chain, DYNC2H1, was originally identified in sea urchin embryos by Gibbons and colleagues and was termed DYH1b . It is much less abundant than DYNC1H1 and does not appear to heterodimerize with DYNC1H1; biochemical analyses suggest that DYNC2H1 is a homodimer . DYNC2H1 contains regions characteristic of cytoplasmic dyneins, for example, human DYNC1H1 and DYNC2H1 sequences are similar within both the motor region and around the light intermediate chain–binding site . However, the expression of its mRNA increases during embryonic reciliation, a property typical of axonemal dyneins, suggesting a flagellar role for an otherwise cytoplasmic-like dynein heavy chain. The flagellar properties of DYNC2H1 were clarified with its identification as the motor responsible for retrograde (tip to base) IFT, in Chlamydomonas, a process required for assembly and maintenance of the eukaryotic cilium/flagellum [6,22]. DYNC2H1 is also important in modified ciliary structures such as nematode mechanosensory neurons  and vertebrate photoreceptors [63,64]. In C. elegans, the DYNC2H1 homolog, che-3, is expressed in ciliated sensory neurons which are thought to be involved in odorant chemotaxis . Mutations of che-3 affect IFT, the establishment and maintenance of sensory cilia, which are stunted and swollen in the mutants, [62,66], chemotactic behavior , and formation of the third larval stage, dauer formation .
The first mammalian DYNC2H1 gene was described in rat, designated DLP4 , and full-length sequence has been obtained . Genetic and biochemical studies suggest that DYNC2H1 associates with a member of the light intermediate chain family, DYNC2LI1 (Figure 1B, and see discussion of the light intermediate chain family below) [14,16,70–73] and possibly also with DYNLL1 (LC8) light chain . In mice Dync2h1, mRNA is abundant in the olfactory epithelium and the ependymal layer of the neural tube; antibodies against DYNC2H1 and DYNC2LI1 strongly stain these tissues and connecting cilia in the retina as well as primary cilia of non-neuronal cultured cells . The co-localization of DYNC2H1, DYNC2LI1, and homologs of the IFT pathway in mammalian ciliated tissues supports a specific role for DYNC2H1 in the generation and maintenance of mammalian cilia [14,16]. Other antibody studies suggest that DYNC2H1 localizes to the cytoplasm of apical regions of ciliated rat tracheal epithelial cells, but not in the cilia themselves . In non-ciliated human COS cells, antibodies against DYNC2H1 show Golgi localization and induce Golgi dispersion, suggesting a cytoplasmic role for DYNC2H1 .
Cytoplasmic Dynein Intermediate Chain Gene Family (DYNC1I1, DYNC1I2)
Intermediate chains are present in axonemal and/or cytoplasmic dyneins from yeast to mammals (Figure 2B). Protein-sequence data demonstrate evolutionary distant relationships between axonemal and cytoplasmic dynein intermediate chains; for example, rat DYNC1I1 has 48% similarity to the Chlamydomonas IC2 axonemal outer arm dynein intermediate chain encoded by the ODA6 locus [75,76]. Figure 2B shows the dynein intermediate chain protein phylogeny. The intermediate chain sequences fall into two distinct clades, intermediate chains 1 and 2, comprised of vertebrate species only. An alternative placement of a Takifugu sequence, as a member of the intermediate chain 1 clade, is almost as well supported by the data as the placement shown in Figure 2B (49% bootstrap support against 51% support). In view of this and with all non-vertebrate species falling outside these clades, the data suggest a recent evolutionary origin for the split into intermediate chain gene 1 and intermediate chain gene 2, perhaps as part of a “2R” event of genome duplication (see  for review). The absence of an amphibian (Xenopus) intermediate chain 1 protein may be due to the current paucity of X. laevis sequences in the GenBank sequence database (http://www.ncbi.nlm.nih.gov/Genbank).
The cytoplasmic dynein 1 intermediate chains have a molecular weight of ~74 kDa  and associate in the cytoplasmic dynein complex with a stoichiometry of two intermediate chains per complex [40,78]. DYNC1I1 and DYNC1I2 proteins are thought to help assemble the cytoplasmic dynein complex and to bind various cargoes. The intermediate chains interact with the dynein activator, dynactin, via their conserved N-termini . The DYNC1I C-termini contain a WD repeat domain [76,80,81] that is conserved between cytoplasmic and axonemal intermediate chains and is important for intermediate chain–binding to the heavy chains [76,82]. The dynein light chains, DYNLL1 (LC8) and DYNLT1 (Tctex1), bind near the N-termini of the intermediate chains [83–85], and the DYNLRB (Roadblock) light chains bind just upstream of the WD repeat region . The DYNC1I are phosphorylated, and phosphorylation at one site regulates DYNC1I2 interaction with the p150 subunit of dynactin [86,87].
The Chlamydomonas IC2 axonemal intermediate chain was localized to the base of the dynein heavy chain dimer by immunoelectron microscopy . Steffen and colleagues identified a similar location for the cytoplasmic dynein intermediate chain and found that antibodies to it block dynein binding to membrane-bound organelles [89,90]. These data indicate a role for DYNC1I in targeting the dynein complex to various cargoes, including membranous organelles and kinetochores [76,79,89]. In Drosophila, mutations in dynein intermediate chain, Cdic (also referred to as cDic and Dic), lead to larval lethality, demonstrating that this intermediate chain provides an essential function. Cdic mutations dominantly enhance the rough-eye phenotype of Glued, a dominant mutation in the p150 subunit of dynactin . Shortwing (sw) is an allele of the dynein intermediate chain gene but, unlike other Cdic alleles, sw is homozygous viable and gives rise to a recessive, temperature-sensitive defect in eye and wing development .
We note that in Drosophila, the Cdic gene lies in the 19DE region of the X chromosome, adjacent to several dynein intermediate chain-like sequences. These sequences are derived from a 7-kb duplication/deletion event involving Cdic and its proximal gene annexin X, which encodes a cell-surface-adhesion protein . The duplication/deletion of this 7-kb region resulted in the formation of a de novo coding sequence, under the control of a testes-specific promoter, called sperm-specific dynein intermediate chain gene (Sdic) . The de novo region has undergone at least 10-fold tandem duplication, which has given rise to a multi-gene family comprising at least four classes of Sdic gene, of which more than one class is functional .
Cytoplasmic dynein 1 intermediate chain 1, DYNC1I1.
Multiple DYNC1I1 isoforms exist in mammals. They are the products of alternative splicing of the N-terminal region of a single DYNC1I1 gene and phosphorylation [76,79,86]. In humans, alternate splicing may arise from cryptic splice-acceptor sites located within exon 4 of this 17-exon gene . Two DYNC1I1 isoforms were found in rat brain and DYNC1I1 mRNA, and protein isoform expression is regulated during rat brain development, and a single DYNC1I1 isoform is found in testis. DYNC1I1 expression is also cell-specific: cultured rat neurons express at least two DYNC1I1 alternative splicing variants and their phosphorylated isoforms, while cultured glial astrocytes do not express any DYNC1I1 gene products [95–97]. In the mouse, expression of Dync1i1 has been shown to be restricted primarily to the brain, with weak expression in testis , further supporting possible neuronal specificity for Dync1i1. As with the other dynein subunits, the isoform diversity of the intermediate chain is thought to result in specific populations of dynein molecules that have specific functions; for example, both DYNC1I1 isoforms are components of cytoplasmic dynein found in the slow component of axonal transport in the optic nerves . Multiple isoforms of the Drosophila intermediate chains are also produced by alternative splicing of the single gene .
Cytoplasmic dynein 1 intermediate chain 2, DYNC1I2.
Vaughan and Vallee used a partial human cDNA sequence with identity to the already known DYNC1I1 gene as a probe to isolate a rat Dync1i2 cDNA; predicted human and rat DYNC1I2 sequences are 94% identical , and the existence of two genes was supported by mapping data that placed Dync1i1 and Dync1i2 at distinct loci within the mouse genome . Like Dync1i1, Dync1i2 produces different splice isoforms: alternative splice sites lie at two positions within the N-terminal region. The expression of Dync1i2 isoforms is ubiquitous with the rat DYNC1I2C isoform being expressed in all tissues and cells examined [79,94,96,97]. During rat brain development, DYNC1I2C is the only isoform found before E14 (embryonic day 14) and it is often the only isoform observed in cultured cells [96,99]. During nerve growth-factor stimulation of PC12 cell differentiation and neurite extension, there is a change in relative expression levels of the DYNC1I2 isoforms . In the rat optic nerve, it has been shown that the DYNC1I2C isoform is the only intermediate chain involved in the fast component of anterograde transport to the axon tip [95,99].
The strong expression of Dync1i2 in the mouse developing limb bud led to the suggestion that DYNC1I2 may play a role in limb development and digit patterning and/or in establishing cell polarity ; dynein may not do this directly, but may mediate these processes by orientating intracellular components correctly .
Cytoplasmic Dynein Light Intermediate Chain Gene Family (DYNC1LI1, DYNC1LI2, DYNC2LI1)
Figure 2C shows the phylogenetic relationships amongst the dynein light intermediate chain protein sequences from various organisms. The light intermediate chains can be separated into three distinct groups: the two light intermediate chains that are components of cytoplasmic dynein 1, DYNC1LI1 and DYNC1LI2, are more closely related to each other than to the cytoplasmic dynein 2 light intermediate chain, DYNC2LI1. Hughes and colleagues first proposed the name light intermediate chains for these subunits , although these polypeptides were also referred to as light chains  prior to the discovery of the smaller light chains . The mammalian cytoplasmic dynein complex contains four species with molecular masses of 50–60 kDa that resolve into numerous isoforms on 2D gels [86,102]. The multiple isoforms observed in 1D and 2D gels are thought to be the result of post-translational phosphorylation, although the possibility of alternate splicing has not been eliminated [86,102,103]. A third gene, DYNC2LI1, has recently been described which encodes a protein that appears to exclusively associate with DYNC2H1 in the cytoplasmic dynein 2 complex [14–16,71]. Unlike the other subunits of cytoplasmic dynein, homologs of the DYNC1LIs have not yet been identified in the axonemal dyneins . The function of the DYNC1LIs has yet to be determined, although it has been suggested that they may regulate the interactions of dynein with dynactin, or with sub-cellular cargoes of dynein-mediated motility. DYNC1LI1 and DYNC1LI2 form only homo-oligomers, and their mutually exclusive binding to the N-terminal base of the dynein heavy chain is consistent with a role in cargo binding .
C. elegans appears to have one light intermediate chain (dli-1) for cytoplasmic dynein (DYNC1H1-based complexes), and one (xbx-1) for cytoplasmic dynein 2 (DYNC2H1-based complexes) . dli-1 is required for dynein function during mitosis, pronuclear migration, centrosome separation, and centrosome association with the male pronuclear envelope , as well as retrograde axonal transport. Mutations in dli-1 lead to an accumulation of cargo at axonal terminals . Disruption of xbx-1 results in ciliary defects and causes behavioral abnormalities that are observed in other cilia mutants . Binding of dli-1 to ZYG-12 is thought to be the mechanism for dynein binding to the nuclear envelope .
Cytoplasmic dynein 1 light intermediate chain 1, DYNC1LI1.
DYNC1LI1 was cloned from rat  and found to have a P-loop motif, which is one of the major conserved motifs making up the nucleotide-binding domain found in numerous proteins, including ATPases and kinases . DYNC1LI1, however, lacks other essential motifs associated with ATPase activity, which itself has not been assayed. Tynan showed that pericentrin, a known dynein cargo, binds DYNC1LI1 and not DYNC1LI2 . DYNC1LI and its phospho-isoform are exclusively found with dynein in the slow component of axonal transport in rat optic nerves . In HeLa cells, DYNC1LI1 localizes to the microtubule organizing centre and mitotic spindle, co-localizing with the GTPase Rab4a (which interacts with the central domain of DYNC1LI1 ); thus DYNC1LI1 may be implicated in the regulation of membrane-receptor recycling. Phosphorylation of the Xenopus DYNC1LI has been implicated in regulation of dynein binding to membrane-bound organelles . It is thought that Xenopus melanosomes contain a distinct dynein light intermediate chain protein, possibly a version of DYNC1LI1 . In the chicken (Gallus gallus) DYNC1LI1 has been called DLC-A, as part of the DLC-A group of light chains .
Cytoplasmic dynein 1 light intermediate chain 2, DYNC1LI2.
DYNC1LI2 is paralogous to DYNC1LI1 and is also thought to be post-translationally modified by phosphorylation [86,102,103]. DYNC1LI2 is found in both the fast and slow components of axonal transport in rat optic nerves, although its phospho-isoforms are found only in the slow component of axonal transport. During nerve growth-factor stimulation of PC12 cell differentiation and neurite extension, DYNC1LI2 gene expression is up-regulated , and phosphorylation of both DYNC1LI1 and DYNC1LI2 is increased . Like DYNC1LI1, the chicken (G. gallus) DYNC1LI2 has also been termed DLC-A, as part of the DLC-A group of light chains .
Cytoplasmic dynein 2 light intermediate chain 1, DYNC2LI1.
DYNC2LI1 is a light intermediate chain that was identified in mammals by two groups and was originally designated D2LIC  and LIC3 . DYNC2LI1 is the light intermediate chain that associates with DYNC2H1 in the cytoplasmic dynein 2 complex: Grissom and colleagues observed that DYNC2LI1 co-immunoprecipitated specifically with DYNC2H1 and co-localized with DYNC2H1 at the Golgi apparatus. Mikami and coworkers  found the 350-amino acid LIC3 polypeptide (AAD34055) had a 24% similarity to rat DYNC1LI2 but failed to observe Golgi localization. DYNC2LI1 has been identified in mouse, C. elegans, Drosophila, and Chlamydomonas [14,16]. A targeted deletion of Dync2li1 in mouse affects development, in particular ventral cell fates and axis establishment in the early embryo . In Chlamydomonas, DYNC2LI1 (D1bLIC) is essential for retrograde IFT . As mentioned above, DYNC2LI1 appears to bind exclusively with DYNC2H1; in agreement with this, we find DYNC2LI1 homologs in species that have DYNC2H1. The exclusive association of DYNC2H1 and DYNC2LI1 with one another, and not with any of the other cytoplasmic dynein subunits, emphasizes the distinct cellular identities and roles of these separate DYNC1H1 and DYNC2H1 dynein complexes.
Cytoplasmic Dynein Light Chain Gene Families
There are three known dynein light chain gene families that are components of cytoplasmic dynein 1: (1) the t-complex–associated family (DYNLT1, DYNLT3), (2) the Roadblock family (DYNLRB1, DYNLRB2), and (3) the LC8 family (DYNLL1, DYNLL2). The gene families are named according to their original discovery, through the effect of mutations in mouse (t-complex associated, Tctex1) and Drosophila (Roadblock), or according to the size of the protein in Chlamydomonas (LC8) as discussed below. We present each family by molecular weight, starting with the largest light chain protein gene family, the t-complex–associated family (~113 amino acids), through to the Roadblock family (~96 amino acids) and the smallest light chain proteins, the LC8 family (~89 amino acids). As described below, some of the light chains have cellular functions that are independent of their role in the cytoplasmic dynein 1 complex.
Cytoplasmic Dynein Light Chain Tctex1 Gene Family (DYNLT1, DYNLT3)
Figure 2D shows the phylogenetic relationships amongst the dynein light chain Tctex1-family protein sequences from various organisms. Our phylogeny shows distinct clades for DYNLT1-like and DYNLT3-like sequences. Tctex2-like sequences lie closer to the outgroup than they do to the DYNLT1 and DYNLT3 clades (not shown).
Cytoplasmic dynein light chain Tctex1, DYNLT1.
Tctex1 (t-complex testis-expressed) gene was originally identified within the mouse t-complex (a 30- to 40-Mb region of Mmu17) as a candidate for one of the “distorter” products responsible for the non-Mendelian transmission of variant t haplotypes . Lader et al.  and O'Neill and Artzt  found evidence of four copies of Dynlt1 (Tctex1) in the mouse genome; we found that the current genomic sequence databases appear to contain only one such locus that maps to Mmu 17, although a processed pseudogene has also been described on Mmu6. Subsequently, DYNLT1 was found to be an integral component of cytoplasmic dynein , and has since also been identified within axonemal inner and outer arm dyneins [117,118]. DYNLT1 binds to the N-terminus of the intermediate chain DYNC1I . Many studies have identified DYNLT1 as a binding partner for various cellular proteins, and it has been suggested that it may attach specific proteins or cellular components to cytoplasmic dynein; for example, DYNLT1, but not its homolog DYNLT3 (see below), binds to the C-terminal domain of rhodopsin and is required for the trafficking of this visual pigment within photoreceptors . The two DYNLT1 polypeptides in the cytoplasmic dynein complex dimerize, and their dimer structure is similar to that of the DYNLL1, LC8, dimer [116,120–122]. The evidence suggests that the same Dynlt1 gene product is a component of both axonemal and cytoplasmic dyneins in mouse . The binding site on DYNC1I for DYNLT1 has been mapped to a 19-amino acid region at the N-terminus .
The Schizosaccharomyces pombe DYNLT-like gene SPAC1805.08 (also referred to as Dlc1) is involved in movement of nuclear material during meiotic prophase and is expressed in astral microtubules and microtubule-anchoring sites on the cell cortex. The Dlc1 localization pattern is similar to that of cytoplasmic dynein heavy chain Dhc1 . Dlc1 null mutants are viable but have irregular nuclear movement during meiosis and defects in sporulation, recombination, and karyogamy . Genetic analyses in Drosophila, which appears to have only one member of the DYNLT family, suggest that DYNLT1 is not essential for cytoplasmic dynein function, as the null mutation is not lethal. However, the mutants do have sperm-motility defects, suggesting they do have an essential role in axonemal dynein [124,125]. In Chlamydomonas, Tctex1 is an axonemal inner arm dynein component , and recently a variant form has been identified in axonemal outer arm dynein (DiBella et al., in press).
Cytoplasmic dynein light chain, DYNLT3.
Closely related to DYNLT1 is DYNLT3, also known as rp3 because it was initially a candidate for causing X-linked retinitis pigmentosa type 3 . However, the actual gene that is defective in this disease was later identified as a guanine nucleotide exchange factor that is unrelated to DYNLT3 . Subsequently, King and colleagues found that DYNLT3 is a cytoplasmic dynein light chain that is differentially expressed in a cell- and tissue-specific manner [78,116]. Interestingly, while many proteins have been identified as binding partners for DYNLT1, none have been identified as binding exclusively to DYNLT3, though recently the Herpes simplex virus capsid protein VP26 has been shown to bind both DYNLT1 and DYNLT3 . There is no evidence that DYNLT3 is a component of axonemal dyneins.
Axonemal dynein light chain, Tctex2.
To avoid confusion with Tctex2, an axonemal dynein subunit, the DYNLT2 designation is not used: a third human t-complex testis-expressed gene, originally characterized by Rappold and colleagues [129,130], was given the name Tctex2, and is also known as LC2, TCTE3, and Tcd3. Patel-King and colleagues demonstrated that it has 35% identity to the 19,000-Mr (relative mobility) axonemal outer arm dynein light chain (LC2) of Chlamydomonas , and that it is distantly related to cytoplasmic light chains DYNLT1 and DYNLT3 [116,120]. LC2 is essential for outer arm dynein assembly . There is evidence that Tctex2 may interact substoichiometrically with cytoplasmic dynein, but there has not yet been a definitive demonstration that it is a cytoplasmic dynein subunit.
In mice, expression of Tctex2 is testis-specific, particularly in later spermatogenic stages, and isoforms are thought to be generated by alternative splicing . As yet, isoforms of the human homolog have not been identified, and its expression is restricted to tissues containing cilia and flagella . Mutations in Tctex2 have been implicated in the autosomal recessive disorder primary ciliary dyskinesia, which results in the impairment of ciliary and flagellar function, although these mutations are thought not to be the primary cause of the disorder .
Mouse Tctex2 lies within the Mmu17 t-complex in a central region containing the distorter/sterility locus Tcd3 . Human Tctex2 maps to the long arm of Chromosome 6  and, interestingly, is a neighbor of the two genes, TCP1 and TCP10, which are also homologs of mouse t-complex loci found adjacent to mouse Tctex2. This conservation of gene order suggests that the region of Chromosome 6q containing these genes is syntenic to the homologous central region of mouse Chromosome 17. In contrast, DYNLT1 and DYNLT3 are located on human Chromosome 6p and show synteny to the distal portion of the mouse t-complex, suggesting that the middle and distal portions of the mouse t-complex are syntenic to the long and short arms of human Chromosome 6, respectively .
Cytoplasmic Dynein Light Chain Roadblock Gene Family (DYNLRB1, DYNLRB2)
The first Roadblock gene was identified in Drosophila through mutational analyses, and from biochemical and sequence comparisons with the Chlamydomonas outer arm dynein LC7a light chain [135,136]. Drosophila has at least six Roadblock homologs, including bithoraxoid, which has been implicated in thoracic and abdominal parasegment development. These proteins belong to an ancient family that has been implicated in NTPase regulation in bacteria . Mutations in the Roadblock genes result in the accumulation of axonal cargoes, mitotic defects, female sterility, and either larval or pupal lethality . Roadblock mutations also affect neuroblast proliferation and result in reduced dendritic complexity, as well as in defects in axonal transport . Mutational analysis in Chlamydomonas suggests that DYNLRB (LC7a) is involved in axonemal outer arm dynein assembly, and a related protein (LC7b) is associated with dynein regulatory elements [136,139].
Figure 2E shows the phylogenetic relationships amongst the dynein light chain Roadblock-family protein sequences from various organisms. The Roadblock sequences are remarkably well conserved between different organisms, with 96% of pair-wise sequence comparisons amongst all sequences shown in Figure 2E demonstrating an identity greater than 50% (data not shown). The high conservation of Roadblock-family sequences presumably arises from functional constraints on the proteins. We note that genes in mammals and in other species incorporate conserved and complete Roadblock sequences (known as Roadblock domains) within their coding regions [135,137]. However, these genes are not thought to be cytoplasmic dyneins; for example, MAPBPIP in human and mouse appears to function mainly in the endosome/lysosome pathway . Both DYNLRB polypeptides are found in mammalian cytoplasmic dynein, but it is not yet known if just one, or both, are utilized in mammalian axonemal dyneins.
Cytoplasmic dynein light chain Roadblock1, DYNLRB1.
Database searches [135,141] (Figure 2E) revealed there are two Roadblock-related proteins in mammals, DYNLRB1 and DYNLRB2 (also termed DYNLC2A and DYNLC2B) . Biochemical studies suggest that in mammals both Roadblocks exist as homo- and heterodimers that associate with cytoplasmic dynein  through specific binding sites on the intermediate chains, distinct from those for the DYNLL (LC8) and DYNLT (Tctex1) light chains . Expression studies in humans have identified tissue-specific differences in the expression of the two human Roadblock-like genes, with strong expression of DYNLRB1 in heart, liver, and brain, and up-regulation in hepatocellular carcinoma tissues . In a role that may be independent of its association with cytoplasmic dynein, TGFb phosphorylation of human DYNLRB1 (termed mLC7–1/km23 by Tang and colleagues ) results in the human DYNLRB1 binding to the TGFb receptor that mediates TGFb responses including JNK activation, c-JUN phosphorylation, and growth inhibition.
Cytoplasmic Dynein Light Chain LC8 Gene Family (DYNLL1, DYNLL2)
Cytoplasmic dynein light chain LC8 1, DYNLL1.
DYNLL (the light chain that has been known as LC8, as well as LC8a and PIN) is a component of many enzyme systems, and it has a long and somewhat confusing history. This protein was originally identified, using biochemical methods, as a light chain of the Chlamydomonas axonemal outer arm dynein [145,146]. The term LC8 derives from the observation that this component migrates at ~8 kDa in SDS-PAGE gels, and it is also the smallest of the eight light chains then known within this Chlamydomonas axonemal dynein. It was first cloned from Chlamydomonas, and closely related sequences were identified in mouse and nematode along with more distantly related proteins in higher plants [147,148]. Using biochemical and immunochemical methods, DYNLL was also identified as an integral component of brain cytoplasmic dynein . Only recently, it has been realized that mammals have two closely related DYNLL genes, and that the protein products of both genes are components of cytoplasmic dynein [148,149]. Thus, most of the studies on the cellular roles of DYNLL do not distinguish between the two DYNLL polypeptides.
Another factor complicating efforts to elucidate the role of the DYNLL polypeptides in dynein function was the realization that large amounts of DYNLL1 in brain, and presumably cells in general, are not associated with the dynein complex . In fact, the DYNLL polypeptides have other important functions unrelated to their role in axonemal and cytoplasmic dyneins. DYNLL1 is a subunit of the flagellar radial spokes which are involved in control of axonemal dynein motor function . DYNLL1 is also a substrate of a p21-activating kinase, and its interaction with the kinase may be important for cell survival . A DYNLL is an integral component of the actin-based motor myosin V . Immunostaining shows that a DYNLL is concentrated in dendritic spines and growth cones, and it is proposed that this is due to its association with the actin-based motor myosin V . DYNLL1 was identified within neuronal nitric oxide synthase (nNOS)  and named “PIN” for “protein inhibitor of nNOS” . However, it is unclear whether it is actually an inhibitor of nNOS or is merely a component of the nNOS complex, as DYNLL1 appears to be required for the stability of various multimeric enzyme complexes. DYNLL1 has been found to interact with a wide variety of other cytoplasmic components, including the pro-apoptotic factor Bim , Drosophila swallow [155,156], and rabies virus P protein , and it may act to attach them to the dynein and/or myosin-V molecular motors. In addition, there are many other DYNLL-interacting proteins not mentioned here that have been identified using yeast two-hybrid screens and other methods.
There are two copies of DYNLL in the cytoplasmic dynein complex, and the crystal and NMR structures of the DYNLL dimer with bound peptide are known [104,158–160]. Both monomers contribute to the formation of two symmetrical grooves in the dimer that are the binding sites for two DYNC1I polypeptides reviewed in . Adding DYNLL to an N-terminal polypeptide of DYNC1I in vitro increases the structural order of DYNC1I, suggesting that DYNLL is important for the assembly of a functional dynein complex .
Figure 2F shows the phylogenetic relationships amongst the dynein light chain LC8-family protein sequences from various organisms. Our phylogeny shows that the mammalian LC8 light chain family falls into two distinct clades containing DYNLL1- and DYNLL2-like genes. DYNLL is highly conserved from alga and humans, and homologs are required for sensory axon projection and other developmental events in Drosophila [162,163], nuclear migration in Aspergillus , and retrograde IFT in Chlamydomonas . The phenotype of partial loss-of-function mutants in Drosophila revealed a wide array of pleiomorphic developmental defects; the total loss-of-function mutation was embryonic lethal . The Drosophila dynein light chain 1 (Cdlc1, also known as ddlc1 and “cut-up” [ctp]) is ubiquitously expressed during development and in adult tissue, and is required for proper embryogenesis and cellular differentiation. Mutations in this gene result in female sterility, which may be due to the severely disordered cytoskeletons of ovarian and embryonic cells . A high degree of sequence similarity (92%) exists between Drosophila Cdlc1 and the 8-kDa flagellar outer arm dynein light chain from Chlamydomonas, and with human and C. elegans light chain 1 (91%), suggesting this gene has been under strong selective pressure . S. pombe has a single known DYNLL homolog, SPAC926.07c (also referred to as Dlc2); it is transcribed during the vegetative phase, induced at low level in the sexual phase, and is enriched at the nuclear periphery . A Dlc2 null mutant has been described with marginally reduced recombination in meiosis, but no other reported phenotype .
During the course of homology searches for this paper, we noted that DYNLL1 has related sequences in several locations in the human genome (data not shown); none of these appear to be associated with expressed sequences and thus may be pseudogenes. There was also a discrepancy in the likely mapping position of DYNLL1, and therefore we carried out a sequence analysis of DYNLL1-related genomic loci and show that the cognate human locus lies on Hsa12q24.31 (data not shown), which agrees with the mouse mapping result of Dynll1 on Mmu5.
Cytoplasmic dynein light chain LC8 2, DYNLL2.
DYNLL2, also known as DYNLL2 and LC8b, is the second member of this light chain family. It was identified by micro-sequencing of polypeptides from purified brain cytoplasmic dynein  and a yeast two-hybrid screen . Mammalian DYNLL1 and DYNLL2 have 93% identity, differing by only six amino acids out of 89. Indicative of the extraordinary conservation of these proteins, the amino acid sequences of both DYNLL1 and DYNLL2 from human, mouse, rat, pig, and cow are identical . Human DYNLL2 was identified in a yeast two-hybrid screen using the guanylate kinase–associated protein (GKAP) as bait and may mediate the interaction between GKAP and actin- and microtubule-based motors, allowing GKAP and its associated proteins to be translocated as a cargo, although DYNLL1 also binds to GKAP . DYNLL2 binds the pro-apoptotic factor Bmf, which binds Bcl2, neutralizing its antiapoptotic activity, a role comparable to that reported for the binding of Bim to DYNLL1 . However, it has also been observed that Bim and Bmf have identical binding affinities for both DYNLL1 and DYNLL2 .
It has further been proposed that DYNLL1 binds specifically to the dynein intermediate chain DYNC1I, while DYNLL2 binds to the myosin-V heavy chain. However, DYNLL2 co-purifies with cytoplasmic dynein from various rat tissues , and DYNLL1- and DYNLL2-GST are equally effective in binding myosin V . Furthermore, DYNLL1 and DYNLL2 bind with equal affinity to DYNC1I in pair-wise yeast two-hybrid studies (K. W. Lo and K. K. Pfister, unpublished data). It is not yet known if one, or both, of the DYNLL polypeptides are associated with axonemal dyneins; however, DYNLL1 is enriched in testes and lung—tissues that have large numbers of cilia or flagella .
Human and Mouse Cytoplasmic Dyneins: Nomenclature, Map Positions, and Sequences
To create Table 1, we cataloged, by literature searches, all known gene and protein names for the cytoplasmic dyneins in mouse and human. In addition, aliases were recorded from the single-query interface LocusLink (http://www.ncbi.nlm.nih.gov/LocusLink) and the Mouse Genome Informatics (MGI) website (http://www.informatics.jax.org). We also included aliases previously approved by the HUGO Gene Nomenclature Committee (http://www.gene.ucl.ac.uk/nomenclature) as well as aliases referenced in sequence submissions to the GenBank (http://www.ncbi.nlm.nih.gov/Genbank) and Entrez (http://www.ncbi.nlm.nih.gov/entrez) sequence databases .
Human and mouse orthologs in Table 1 are taken from the literature and databases. Human and mouse chromosomal locations were obtained from the literature and from the MGI and LocusLink databases. The OMIM numbers given for gene and disease loci in humans refers to the unique accession numbers in the On-line Mendelian Inheritance in Man database (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM). Nucleotide and protein sequences (prefix NM_ and NP_, respectively) are National Center for Biotechnology Information (NCBI) Reference Sequence (RefSeq, http://www.ncbi.nlm.nih.gov/RefSeq) and Swiss-Prot accession numbers (http://www.ebi.ac.uk/swissprot), respectively . The NCBI RefSeq project provides a non-redundant and comprehensive collection of nucleotide and protein sequences drawn from the primary-sequence database GenBank. RefSeq collates and summarizes primary-sequence data to give a minimal tiling path for individual transcripts, using available cDNA and genomic sequence whilst removing mutations, sequencing errors, and cloning artifacts. Sequences are validated in silico by NCBI's Genome Annotation project to confirm that any genomic sequence incorporated into a RefSeq cDNA matches primary cDNA sequences in GenBank, and that the coding region really can be translated into the corresponding protein sequence. Accession numbers beginning with the prefix XM_ (mRNA) and XP_ (protein) are RefSeq sequences of transcripts and proteins that are annotated on NCBI genomic contigs; these may have incomplete cDNA-tiling-sequence data or contig sequences . For dyneins with known isoforms, isoform-sequence accession numbers available within nucleotide and protein databases are given.
Included in the heavy chains that we found were “Cell Division Cycle 23, yeast homolog” (CDC23) and “Cell Division Cycle 22, yeast homolog” (CDC22), which are GenBank aliases for human and mouse dynein heavy chain 1, respectively. We found no evidence in the literature to support the “CDC” designation of these genes and their products in terms of either “Cell Division Cycle” or “Cytoplasmic Dynein Chain”. We compared mouse and human heavy chain 1 cDNA and protein sequences with mouse, human, and yeast CDC23 and CDC22 sequences and found no similarity to support this designation (data not shown). We concluded that the synonym CDC had most likely been attributed in error, and we contacted NCBI who, in agreement with our findings, removed the CDC designation from the sequences involved.
Human/Mouse Homology Searches
Homology searches of human cytoplasmic dynein subunit genes were conducted using position-specific iterative BLAST (PSI-BLAST)  at NCBI (http://www.ncbi.nlm.nih.gov/BLAST; Table 2). The PSI-BLAST program identifies families of related proteins using an iterative BLAST procedure . In an initial search, a position-specific scoring matrix is constructed from a multiple sequence alignment of the highest scoring hits. Subsequent iterations using the position-specific scoring matrix are performed in a new BLAST query to refine the profile and find additional related sequences. We used nucleotide and protein sequences from each known human dynein gene to query the human and mouse non-redundant sequence databases at GenBank, using default parameters and the BLOSUM-62 substitution matrix, which has been shown to be the most effective substitution matrix to identify new members of a protein family . Where dynein isoforms were present, the longest sequence was used to search the databases.
To establish gene family groupings, we investigated the phylogenetic relationships between dynein protein homologs in various organisms. Homologous sequences were identified by searching the GenBank non-redundant protein database, with the human protein using PSI-BLAST with default parameters and the BLOSUM-62 substitution matrix. Searches of pufferfish sequence Takifugu rubripes (commonly known as Fugu rubripes), for which little transcribed sequence exists although a usable genome assembly is present, were performed using the BLAST (TBLASTN) feature at the Ensembl Fugu Genome Browser (version 2.0; http://www.ensembl.org/Fugu_rubripes), searching with human protein sequence against a translated nucleotide database.
Protein sequences were aligned for comparison across their full lengths using the multiple sequence alignment program CLUSTALW  (http://www.ebi.ac.uk/clustalw) and applying the GONNET250 matrix as default. The GONNET250 is a widely used matrix for performing protein-sequence alignments, allowing 250 accepted point mutations per 100 amino acids, using scoring tables based on the PAM250 matrix .
Two different phylogenetic methods were used to analyse the dynein gene family alignments. Maximum-likelihood trees were inferred under the Jones, Taylor, and Thornton (JTT) empirical model of amino-acid substitution using PHYML version 2.4.3 , as was non-parametric bootstrapping using 100 resampled alignments for each gene family. Bayesian analyses were performed using MrBayes version 3.0B4 , using the default Bayesian priors on tree topologies and branch lengths. Two different sets of analyses were performed for each gene family, the first allowing the Markov-chain Monte-Carlo algorithm to move between the 11 different amino-acid substitution models available in MrBayes, and another specifying the JTT model. The first analysis allows the chain to take into account uncertainty in the substitution process. For all analyses performed here, the posterior probability of the JTT model was at least 99%, confirming that this model best describes the evolution of the dynein sequences—so only results from the fixed-JTT model analyses are shown here.
For each analysis, three chains of 1,000,000 generations each were run, sampling parameters every 100 generations and discarding the first 100,000 generations as a burn-in period. Running these multiple independent chains allowed visual confirmation that the chains had reached a stationary state by ensuring that all three chains were moving around a region of similar likelihood. For one of the gene families (cytoplasmic dynein heavy chain), the three chains had reached different likelihood values after 1,000,000 generations, suggesting failure to converge. Running another three independent chains resulted in five out of six chains agreeing on the likelihood values, suggesting that only one chain had not converged properly. In all cases, the phylogeny presented is the majority-rule consensus of the posterior sample of tree topologies from all three Markov chains, drawn using TreeView  with posterior clade probabilities and maximum-likelihood bootstrap values shown for each clade on these trees.
Searching for Function and Mutant Phenotypes
As well as literature searches, information on protein function was taken from the Gene Ontology database (http://www.geneontology.org), which provides data on function and processes associated with a search protein. Mutant-phenotype data were obtained from the literature and the following sources: Online Mendelian Inheritance in Man at NCBI for human (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM); MGI for mouse (http://www.informatics.jax.org); FlyBase for Drosophila (http://www.flybase.org); and WormBase for C. elegans (http://www.wormbase.org).
In this paper, we have provided an overview of the two cytoplasmic dynein complexes, cytoplasmic dynein 1 and cytoplasmic dynein 2, from a genetic perspective. We have highlighted the unique subunit compositions and cellular functions of the two cytoplasmic dyneins, and we have emphasized the unique role of cytoplasmic dynein 2 in IFT. We have described the different mammalian dynein gene families, and have shown the phylogenetic and functional relationships between members of individual families. We carried out initial database searches and clarified and corrected anomalous data. We have also discussed known functions and mutations of these proteins, and we have highlighted both their fundamental importance to the cell and the fact that much research remains to be carried out to define the roles of individual proteins.
Table S1. Species Names, NCBI/GenBank Protein-Sequence Accession Numbers, and NCBI/GenBank Gene/Protein Names for Figures 2A–F
(53 KB DOC)
The Entrez Gene database (http://www.ncbi.nlm.nih.gov/entrez) accession numbers for the proteins discussed in this paper are Cdic (also referred to as cDic and Dic) (44160); che-3 (DYNC2H1 homolog) (172593); DYNC1I1 (1780); DYNC1I2 (1781); DYNC1LI1 (51143); DYNC1LI2, (1783); DYNC2H1, (79659); DYNC2LI1 (51626); DYNLL1 (LC8) (8655); DYNLL2 (also known as DYNLL2 and LC8b) (140735); DYNLRB1 (also termed DYNLC2A) (83658); DYNLRB2 (also termed DYNLC2B) (83657); DYNLT1 (Tctex1) (6993); MAPBPIP (28956); SPAC1805.08 (also referred to as Dlc1) (3361491).
The Entrez Gene database (http://www.ncbi.nlm.nih.gov/entrez) accession numbers for the genes discussed in this paper are Dhc64C (38580); dli-1 (178260); dyn1 (853928); Dync1h1 (13424); DYNC1H1 (1778) ; Dync1i1 (13426); Dync1i2 (13427); Dync2li1 (213575); Dynlt1 (Tctex1) in the mouse genome (21648); DYNLT3 (6990); human Tctex2 (also known as LC2, TCTE3, and Tcd3) (6991); mouse Tctex2 (21647); xbx-1 (184080).
The Entrez Protein database (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=protein&cmd=search&term=) accession numbers for the proteins discussed in this paper are C. elegans LC8 sequence (49822); C. elegans light chain 1 (498422); Cdlc1 (525075); Chlamydomonas 19,000-Mr axonemal outer arm dynein light chain (LC2) (AAB58383); rat DYNC1I1 (062107); rat DYNC1LI2 (112288).
The OMIM (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM) accession numbers for the proteins discussed in this paper are autosomal recessive disorder primary ciliary dyskinesia (242650); Bim (603827); Bmf (606266); X-linked retinitis pigmentosa type 3 (300389).
The Ensembl (http://www.ensembl.org/Fugu_rubripes/textview) accession number for the Takifugu LC8 sequence is SINFRUP0000015498.
The SwissProt (http://ca.expasy.org/sprot/) accession numbers for the Chlamydomonas 8-kDa flagellar outer arm dynein light chain and the Chlamydomonas LC2 light chain used as the outgroup in Figure 2 are Q39580 and T08216, respectively.
PRS, HH, and EMCF are supported by the UK Medical Research Council, the Motor Neurone Disease Association, and the American Amyotrophic Lateral Sclerosis Association. KKP is supported by a grant from the National Institute of Neurological Disorders and Stroke, at the National Institutes of Health (NIH). SMK is supported by grants (GM51293 and GM63548) from the National Institutes of General Medical Sciences, NIH, and is an investigator of the Patrick and Catherine Weldon Donaghue Medical Research Foundation. JC is supported by the Biotechnology and Biological Sciences Research Council (BBSRC), grant 40/G18385. AR is supported by grants from the BBSRC and the Royal Society. We are most grateful to Lois Maltais of the Mouse Genomic Nomenclature Committee and to Mathew Wright of the Human Genome Organization Gene Nomenclature Committee for their help and support in preparing this manuscript. We thank Ray Young for supplying graphics.
- 1. Gibbons IR (1965) Chemical dissection of cilia. Arch Biol (Liege) 76: 317–352.
- 2. Sale WS, Satir P (1977) Direction of active sliding of microtubules in Tetrahymena cilia. Proc Natl Acad Sci U S A 74: 2045–2049.
- 3. Paschal BM, Shpetner HS, Vallee RB (1987) MAP 1C is a microtubule-activated ATPase which translocates microtubules in vitro and has dynein-like properties. J Cell Biol 105: 1273–1282.
- 4. Paschal BM, King SM, Moss AG, Collins CA, Vallee RB, et al. (1987) Isolated flagellar outer arm dynein translocates brain microtubules in vitro. Nature 330: 672–674.
- 5. Paschal BM, Vallee RB (1987) Retrograde transport by the microtubule-associated protein MAP 1C. Nature 330: 181–183.
- 6. Pazour GJ, Dickert BL, Witman GB (1999) The DHC1b (DHC2) isoform of cytoplasmic dynein is required for flagellar assembly. J Cell Biol 144: 473–481.
- 7. Sakakibara H, Kojima H, Sakai Y, Katayama E, Oiwa K (1999) Inner arm dynein c of Chlamydomonas flagella is a single-headed processive motor. Nature 400: 586–590.
- 8. Gibbons IR (1995) Dynein family of motor proteins: Present status and future questions. Cell Motil Cytoskeleton 32: 136–144.
- 9. Vallee RB, Williams JC, Varma D, Barnhart LE (2004) Dynein: An ancient motor protein involved in multiple modes of transport. J Neurobiol 58: 189–200.
- 10. Cole DG (2003) The intraflagellar transport machinery of Chlamydomonas reinhardtii. Traffic 4: 435–442.
- 11. Karki S, Holzbaur EL (1999) Cytoplasmic dynein and dynactin in cell division and intracellular transport. Curr Opin Cell Biol 11: 45–53.
- 12. King SJ, Schroer TA (2000) Dynactin increases the processivity of the cytoplasmic dynein motor. Nat Cell Biol 2: 20–24.
- 13. Quintyne NJ, Schroer TA (2002) Distinct cell cycle-dependent roles for dynactin and dynein at centrosomes. J Cell Biol 159: 245–254.
- 14. Grissom PM, Vaisberg EA, McIntosh JR (2002) Identification of a novel light intermediate chain (D2LIC) for mammalian cytoplasmic dynein 2. Mol Biol Cell 13: 817–829.
- 15. Mikami A, Tynan SH, Hama T, Luby-Phelps K, Saito T, et al. (2002) Molecular structure of cytoplasmic dynein 2 and its distribution in neuronal and ciliated cells. J Cell Sci 115: 4801–4808.
- 16. Perrone CA, Tritschler D, Taulman P, Bower R, Yoder BK, et al. (2003) A novel dynein light intermediate chain colocalizes with the retrograde motor for intraflagellar transport at sites of axoneme assembly in Chlamydomonas and mammalian cells. Mol Biol Cell 14: 2041–2056.
- 17. Hafezparast M, Klocke R, Ruhrberg C, Marquardt A, Ahmad-Annuar A, et al. (2003) Mutations in dynein link motor neuron degeneration to defects in retrograde transport. Science 300: 808–812.
- 18. Puls I, Jonnakuty C, LaMonte BH, Holzbaur EL, Tokito M, et al. (2003) Mutant dynactin in motor neuron disease. Nat Genet 33: 455–456.
- 19. Munch C, Sedlmeier R, Meyer T, Homberg V, Sperfeld AD, et al. (2004) Point mutations of the p150 subunit of dynactin (DCTN1) gene in ALS. Neurology 63: 724–726.
- 20. HUGO Gene Nomenclature Committee (2004) HGNC database symbol report: DYNC1H1synonym entry. London: HUGO Gene Nomenclature Committee, University College London. Available: http://www.gene.ucl.ac.uk/cgi-bin/nomenclature/get_data.pl?hgnc_id=2961. Accessed 25 November 2005.
- 21. Ohara O, Nagase T, Ishikawa K, Nakajima D, Ohira M, et al. (1997) Construction and characterization of human brain cDNA libraries suitable for analysis of cDNA clones encoding relatively large proteins. DNA Res 4: 53–59.
- 22. Porter ME, Bower R, Knott JA, Byrd P, Dentler W (1999) Cytoplasmic dynein heavy chain 1b is required for flagellar assembly in Chlamydomonas. Mol Biol Cell 10: 693–712.
- 23. Vaisberg EA, Grissom PM, McIntosh JR (1996) Mammalian cells express three distinct dynein heavy chains that are localized to different cytoplasmic organelles. J Cell Biol 133: 831–842.
- 24. Bloom GS, Schoenfeld TA, Vallee RB (1984) Widespread distribution of the major polypeptide component of MAP 1 (microtubule-associated protein 1) in the nervous system. J Cell Biol 98: 320–330.
- 25. Neuwald AF, Aravind L, Spouge JL, Koonin EV (1999) AAA+: A class of chaperone-like ATPases associated with the assembly, operation, and disassembly of protein complexes. Genome Res 9: 27–43.
- 26. Neely MD, Erickson HP, Boekelheide K (1990) HMW-2, the Sertoli cell cytoplasmic dynein from rat testis, is a dimer composed of nearly identical subunits. J Biol Chem 265: 8691–8698.
- 27. Samso M, Radermacher M, Frank J, Koonce MP (1998) Structural characterization of a dynein motor domain. J Mol Biol 276: 927–937.
- 28. Samso M, Koonce MP (2004) 25 Angstrom resolution structure of a cytoplasmic dynein motor reveals a seven-member planar ring. J Mol Biol 340: 1059–1072.
- 29. Mitchell DR, Brown KS (1994) Sequence analysis of the Chlamydomonas alpha and beta dynein heavy chain genes. J Cell Sci 107: 635–644.
- 30. Sakato M, King SM (2004) Design and regulation of the AAA+ microtubule motor dynein. J Struct Biol 146: 58–71.
- 31. Saraste M, Sibbald PR, Wittinghofer A (1990) The P-loop—A common motif in ATP- and GTP-binding proteins. Trends Biochem Sci 15: 430–434.
- 32. Eshel D (1995) Functional dissection of the dynein motor domain. Cell Motil Cytoskeleton 32: 133–135.
- 33. Kon T, Nishiura M, Ohkura R, Toyoshima YY, Sutoh K (2004) Distinct functions of nucleotide-binding/hydrolysis sites in the four AAA modules of cytoplasmic dynein. Biochemistry 43: 11266–11274.
- 34. Mocz G, Gibbons IR (1996) Phase partition analysis of nucleotide binding to axonemal dynein. Biochemistry 35: 9204–9211.
- 35. Takahashi Y, Edamatsu M, Toyoshima YY (2004) Multiple ATP-hydrolyzing sites that potentially function in cytoplasmic dynein. Proc Natl Acad Sci U S A 101: 12865–12869.
- 36. Gee MA, Heuser JE, Vallee RB (1997) An extended microtubule-binding structure within the dynein motor domain. Nature 390: 636–639.
- 37. Burgess SA, Walker ML, Sakakibara H, Knight PJ, Oiwa K (2003) Dynein structure and power stroke. Nature 421: 715–718.
- 38. Tynan SH, Purohit A, Doxsey SJ, Vallee RB (2000) Light intermediate chain 1 defines a functional subfraction of cytoplasmic dynein which binds to pericentrin. J Biol Chem 275: 32763–32768.
- 39. Habura A, Tikhonenko I, Chisholm RL, Koonce MP (1999) Interaction mapping of a dynein heavy chain. Identification of dimerization and intermediate chain binding domains. J Biol Chem 274: 15447–15453.
- 40. Susalka SJ, Nikulina K, Salata MW, Vaughan PS, King SM, et al. (2002) The roadblock light chain binds a novel region of the cytoplasmic Dynein intermediate chain. J Biol Chem 277: 32939–32946.
- 41. Mikami A, Paschal BM, Mazumdar M, Vallee RB (1993) Molecular cloning of the retrograde transport motor cytoplasmic dynein (MAP 1C). Neuron 10: 787–796.
- 42. Zhang Z, Tanaka Y, Nonaka S, Aizawa H, Kawasaki H, et al. (1993) The primary structure of rat brain (cytoplasmic) dynein heavy chain, a cytoplasmic motor enzyme. Proc Natl Acad Sci U S A 90: 7928–7932.
- 43. Vaisberg EA, Koonce MP, McIntosh JR (1993) Cytoplasmic dynein plays a role in mammalian mitotic spindle formation. J Cell Biol 123: 849–858.
- 44. Harada A, Takei Y, Kanai Y, Tanaka Y, Nonaka S, et al. (1998) Golgi vesiculation and lysosome dispersion in cells lacking cytoplasmic dynein. J Cell Biol 141: 51–59.
- 45. Gepner J, Li M, Ludmann S, Kortas C, Boylan K, et al. (1996) Cytoplasmic dynein function is essential in Drosophila melanogaster. Genetics 142: 865–878.
- 46. Li M, McGrail M, Serr M, Hays TS (1994) Drosophila cytoplasmic dynein, a microtubule motor that is asymmetrically localized in the oocyte. J Cell Biol 126: 1475–1494.
- 47. McGrail M, Hays TS (1997) The microtubule motor cytoplasmic dynein is required for spindle orientation during germline cell divisions and oocyte differentiation in Drosophila. Development 124: 2409–2419.
- 48. Robinson JT, Wojcik EJ, Sanders MA, McGrail M, Hays TS (1999) Cytoplasmic dynein is required for the nuclear attachment and migration of centrosomes during mitosis in Drosophila. J Cell Biol 146: 597–608.
- 49. Martin M, Iyadurai SJ, Gassman A, Gindhart JG Jr, Hays TS, et al. (1999) Cytoplasmic dynein, the dynactin complex, and kinesin are interdependent and essential for fast axonal transport. Mol Biol Cell 10: 3717–3728.
- 50. Hamill DR, Severson AF, Carter JC, Bowerman B (2002) Centrosome maturation and mitotic spindle assembly in C. elegans require SPD-5, a protein with multiple coiled-coil domains. Dev Cell 3: 673–684.
- 51. Mains PE, Sulston IA, Wood WB (1990) Dominant maternal-effect mutations causing embryonic lethality in Caenorhabditis elegans. Genetics 125: 351–369.
- 52. Koushika SP, Schaefer AM, Vincent R, Willis JH, Bowerman B, et al. (2004) Mutations in Caenorhabditis elegans cytoplasmic dynein components reveal specificity of neuronal retrograde cargo. J Neurosci 24: 3907–3916.
- 53. Schmidt DJ, Rose DJ, Saxton WM, Strome S (2005) Functional analysis of cytoplasmic dynein heavy chain in Caenorhabditis elegans with fast-acting temperature-sensitive mutations. Mol Biol Cell 16: 1200–1212.
- 54. Mains PE, Kemphues KJ, Sprunger SA, Sulston IA, Wood WB (1990) Mutations affecting the meiotic and mitotic divisions of the early Caenorhabditis elegans embryo. Genetics 126: 593–605.
- 55. Eshel D, Urrestarazu LA, Vissers S, Jauniaux JC, Vliet-Reedijk JC, et al. (1993) Cytoplasmic dynein is required for normal nuclear segregation in yeast. Proc Natl Acad Sci U S A 90: 11172–11176.
- 56. Li YY, Yeh E, Hays T, Bloom K (1993) Disruption of mitotic spindle orientation in a yeast dynein mutant. Proc Natl Acad Sci U S A 90: 10096–10100.
- 57. Saunders WS, Koshland D, Eshel D, Gibbons IR, Hoyt MA (1995) Saccharomyces cerevisiae kinesin- and dynein-related proteins required for anaphase chromosome segregation. J Cell Biol 128: 617–624.
- 58. Lawrence CJ, Morris NR, Meagher RB, Dawe RK (2001) Dyneins have run their course in plant lineage. Traffic 2: 362–363.
- 59. International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome. Nature 436: 793–800.
- 60. Vale RD (2003) The molecular motor toolbox for intracellular transport. Cell 112: 467–480.
- 61. Gibbons BH, Asai DJ, Tang WJ, Hays TS, Gibbons IR (1994) Phylogeny and expression of axonemal and cytoplasmic dynein genes in sea urchins. Mol Biol Cell 5: 57–70.
- 62. Signor D, Wedaman KP, Orozco JT, Dwyer ND, Bargmann CI, et al. (1999) Role of a class DHC1b dynein in retrograde transport of IFT motors and IFT raft particles along cilia, but not dendrites, in chemosensory neurons of living Caenorhabditis elegans. J Cell Biol 147: 519–530.
- 63. Baker SA, Freeman K, Luby-Phelps K, Pazour GJ, Besharse JC (2003) IFT20 links kinesin II with a mammalian intraflagellar transport complex that is conserved in motile flagella and sensory cilia. J Biol Chem 278: 34211–34218.
- 64. Rosenbaum JL, Cole DG, Diener DR (1999) Intraflagellar transport: The eyes have it. J Cell Biol 144: 385–388.
- 65. Bargmann CI, Hartwieg E, Horvitz HR (1993) Odorant-selective genes and neurons mediate olfaction in C. elegans. Cell 74: 515–527.
- 66. Collet J, Spike CA, Lundquist EA, Shaw JE, Herman RK (1998) Analysis of osm-6, a gene that affects sensory cilium structure and sensory neuron function in Caenorhabditis elegans. Genetics 148: 187–200.
- 67. Wicks SR, de Vries CJ, van Luenen HG, Plasterk RH (2000) CHE-3, a cytosolic dynein heavy chain, is required for sensory cilia structure and function in Caenorhabditis elegans. Dev Biol 221: 295–307.
- 68. Albert PS, Brown SJ, Riddle DL (1981) Sensory control of dauer larva formation in Caenorhabditis elegans. J Comp Neurol 198: 435–451.
- 69. Tanaka Y, Zhang Z, Hirokawa N (1995) Identification and molecular evolution of new dynein-like protein sequences in rat brain. J Cell Sci 108: 1883–1893.
- 70. Adams MD, Celniker SE, Holt RA, Evans CA, Gocayne JD, et al. (2000) The genome sequence of Drosophila melanogaster. Science 287: 2185–2195.
- 71. Hou Y, Pazour GJ, Witman GB (2004) A dynein light intermediate chain, D1bLIC, is required for retrograde intraflagellar transport. Mol Biol Cell 15: 4382–4394.
- 72. Pazour GJ, Wilkerson CG, Witman GB (1998) A dynein light chain is essential for the retrograde particle movement of intraflagellar transport (IFT). J Cell Biol 141: 979–992.
- 73. Schafer JC, Haycraft CJ, Thomas JH, Yoder BK, Swoboda P (2003) XBX-1 encodes a dynein light intermediate chain required for retrograde intraflagellar transport and cilia assembly in Caenorhabditis elegans. Mol Biol Cell 14: 2057–2070.
- 74. Criswell PS, Ostrowski LE, Asai DJ (1996) A novel cytoplasmic dynein heavy chain: Expression of DHC1b in mammalian ciliated epithelial cells. J Cell Sci 109: 1891–1898.
- 75. Mitchell DR, Kang Y (1991) Identification of oda6 as a Chlamydomonas dynein mutant by rescue with the wild-type gene. J Cell Biol 113: 835–842.
- 76. Paschal BM, Mikami A, Pfister KK, Vallee RB (1992) Homology of the 74-kD cytoplasmic dynein subunit with a flagellar dynein polypeptide suggests an intracellular targeting function. J Cell Biol 118: 1133–1143.
- 77. Wolfe KH (2001) Yesterday's polyploids and the mystery of diploidization. Nat Rev Genet 2: 333–341.
- 78. King SM, Barbarese E, Dillman JF III, Benashski SE, Do KT, et al. (1998) Cytoplasmic dynein contains a family of differentially expressed light chains. Biochemistry 37: 15033–15041.
- 79. Vaughan KT, Vallee RB (1995) Cytoplasmic dynein binds dynactin through a direct interaction between the intermediate chains and p150Glued. J Cell Biol 131: 1507–1516.
- 80. Wilkerson CG, King SM, Koutoulis A, Pazour GJ, Witman GB (1995) The 78,000 M(r) intermediate chain of Chlamydomonas outer arm dynein is a WD-repeat protein required for arm assembly. J Cell Biol 129: 169–178.
- 81. Yang P, Sale WS (1998) The Mr 140,000 intermediate chain of Chlamydomonas flagellar inner arm dynein is a WD-repeat protein implicated in dynein arm anchoring. Mol Biol Cell 9: 3335–3349.
- 82. Ma S, Trivinos-Lagos L, Graf R, Chisholm RL (1999) Dynein intermediate chain mediated dynein-dynactin interaction is required for interphase microtubule organization and centrosome replication and separation in Dictyostelium. J Cell Biol 147: 1261–1274.
- 83. Lo KW, Naisbitt S, Fan JS, Sheng M, Zhang M (2001) The 8-kDa dynein light chain binds to its targets via a conserved (K/R)XTQT motif. J Biol Chem 276: 14059–14066.
- 84. Makokha M, Hare M, Li M, Hays T, Barbar E (2002) Interactions of cytoplasmic dynein light chains Tctex-1 and LC8 with the intermediate chain IC74. Biochemistry 41: 4302–4311.
- 85. Mok YK, Lo KW, Zhang M (2001) Structure of Tctex-1 and its interaction with cytoplasmic dynein intermediate chain. J Biol Chem 276: 14067–14074.
- 86. Dillman JF III, Pfister KK (1994) Differential phosphorylation in vivo of cytoplasmic dynein associated with anterogradely moving organelles. J Cell Biol 127: 1671–1681.
- 87. Vaughan PS, Leszyk JD, Vaughan KT (2001) Cytoplasmic dynein intermediate chain phosphorylation regulates binding to dynactin. J Biol Chem 276: 26171–26179.
- 88. King SM, Witman GB (1990) Localization of an intermediate chain of outer arm dynein by immunoelectron microscopy. J Biol Chem 265: 19807–19811.
- 89. Steffen W, Hodgkinson JL, Wiche G (1996) Immunogold localisation of the intermediate chain within the protein complex of cytoplasmic dynein. J Struct Biol 117: 227–235.
- 90. Steffen W, Karki S, Vaughan KT, Vallee RB, Holzbaur EL, et al. (1997) The involvement of the intermediate chain of cytoplasmic dynein in binding the motor complex to membranous organelles of Xenopus oocytes. Mol Biol Cell 8: 2077–2088.
- 91. Boylan KL, Hays TS (2002) The gene for the intermediate chain subunit of cytoplasmic dynein is essential in Drosophila. Genetics 162: 1211–1220.
- 92. Nurminsky DI, Nurminskaya MV, Benevolenskaya EV, Shevelyov YY, Hartl DL, et al. (1998) Cytoplasmic dynein intermediate chain isoforms with different targeting properties created by tissue-specific alternative splicing. Mol Cell Biol 18: 6816–6825.
- 93. Ranz JM, Ponce AR, Hartl DL, Nurminsky D (2003) Origin and evolution of a new gene expressed in the Drosophila sperm axoneme. Genetica 118: 233–244.
- 94. Crackower MA, Sinasac DS, Xia J, Motoyama J, Prochazka M, et al. (1999) Cloning and characterization of two cytoplasmic dynein intermediate chain genes in mouse and human. Genomics 55: 257–267.
- 95. Dillman JF III, Dabney LP, Pfister KK (1996) Cytoplasmic dynein is associated with slow axonal transport. Proc Natl Acad Sci U S A 93: 141–144.
- 96. Pfister KK, Salata MW, Dillman JF III, Torre E, Lye RJ (1996) Identification and developmental regulation of a neuron-specific subunit of cytoplasmic dynein. Mol Biol Cell 7: 331–343.
- 97. Pfister KK, Salata MW, Dillman JF III, Vaughan KT, Vallee RB, et al. (1996) Differential expression and phosphorylation of the 74-kDa intermediate chains of cytoplasmic dynein in cultured neurons and glia. J Biol Chem 271: 1687–1694.
- 98. Vaughan KT, Mikami A, Paschal BM, Holzbaur EL, Hughes SM, et al. (1996) Multiple mouse chromosomal loci for dynein-based motility. Genomics 36: 29–38.
- 99. Susalka SJ, Pfister KK (2000) Cytoplasmic dynein subunit heterogeneity: Implications for axonal transport. J Neurocytol 29: 819–829.
- 100. Salata MW, Dillman JF III, Lye RJ, Pfister KK (2001) Growth factor regulation of cytoplasmic dynein intermediate chain subunit expression preceding neurite extension. J Neurosci Res 65: 408–416.
- 101. Levin M, Nascone N (1997) Two molecular models of initial left-right asymmetry generation. Med Hypotheses 49: 429–435.
- 102. Hughes SM, Vaughan KT, Herskovits JS, Vallee RB (1995) Molecular analysis of a cytoplasmic dynein light intermediate chain reveals homology to a family of ATPases. J Cell Sci 108: 17–24.
- 103. Gill SR, Cleveland DW, Schroer TA (1994) Characterization of DLC-A and DLC-B, two families of cytoplasmic dynein light chain subunits. Mol Biol Cell 5: 645–654.
- 104. King SM, Barbarese E, Dillman JF III, Patel-King RS, Carson JH, et al. (1996) Brain cytoplasmic and flagellar outer arm dyneins share a highly conserved Mr 8,000 light chain. J Biol Chem 271: 19358–19366.
- 105. King SJ, Bonilla M, Rodgers ME, Schroer TA (2002) Subunit organization in cytoplasmic dynein subcomplexes. Protein Sci 11: 1239–1250.
- 106. Yoder JH, Han M (2001) Cytoplasmic dynein light intermediate chain is required for discrete aspects of mitosis in Caenorhabditis elegans. Mol Biol Cell 12: 2921–2933.
- 107. Malone CJ, Misner L, Le Bot N, Tsai MC, Campbell JM, et al. (2003) The C. elegans hook protein, ZYG-12, mediates the essential attachment between the centrosome and nucleus. Cell 115: 825–836.
- 108. Walker JE, Saraste M, Runswick MJ, Gay NJ (1982) Distantly related sequences in the alpha- and beta-subunits of ATP synthase, myosin, kinases and other ATP-requiring enzymes and a common nucleotide binding fold. EMBO J 1: 945–951.
- 109. Bielli A, Thornqvist PO, Hendrick AG, Finn R, Fitzgerald K, et al. (2001) The small GTPase Rab4A interacts with the central region of cytoplasmic dynein light intermediate chain-1. Biochem Biophys Res Commun 281: 1141–1153.
- 110. Niclas J, Allan VJ, Vale RD (1996) Cell cycle regulation of dynein association with membranes modulates microtubule-based organelle transport. J Cell Biol 133: 585–593.
- 111. Reilein AR, Serpinskaya AS, Karcher RL, Dujardin DL, Vallee RB, et al. (2003) Differential regulation of dynein-driven melanosome movement. Biochem Biophys Res Commun 309: 652–658.
- 112. Angelastro JM, Klimaschewski L, Tang S, Vitolo OV, Weissman TA, et al. (2000) Identification of diverse nerve growth factor-regulated genes by serial analysis of gene expression (SAGE) profiling. Proc Natl Acad Sci U S A 97: 10424–10429.
- 113. Rana AA, Martinez Barbera JP, Rodriguez TA, Lynch D, Hirst E, et al. (2004) Targeted deletion of the novel cytoplasmic dynein mD2LIC disrupts the embryonic organiser, formation of the body axes and specification of ventral cell fates. Development 131: 4999–5007.
- 114. Lader E, Ha HS, O'Neill M, Artzt K, Bennett D (1989) Tctex-1: A candidate gene family for a mouse t complex sterility locus. Cell 58: 969–979.
- 115. O'Neill MJ, Artzt K (1995) Identification of a germ-cell-specific transcriptional repressor in the promoter of Tctex-1. Development 121: 561–568.
- 116. King SM, Dillman JF III, Benashski SE, Lye RJ, Patel-King RS, et al. (1996) The mouse t-complex-encoded protein Tctex-1 is a light chain of brain cytoplasmic dynein. J Biol Chem 271: 32281–32287.
- 117. Harrison A, Olds-Clarke P, King SM (1998) Identification of the t complex-encoded cytoplasmic dynein light chain Tctex1 in inner arm I1 supports the involvement of flagellar dyneins in meiotic drive. J Cell Biol 140: 1137–1147.
- 118. Kagami O, Gotoh M, Makino Y, Mohri H, Kamiya R, et al. (1998) A dynein light chain of sea urchin sperm flagella is a homolog of mouse Tctex 1, which is encoded by a gene of the t complex sterility locus. Gene 211: 383–386.
- 119. Tai AW, Chuang JZ, Bode C, Wolfrum U, Sung CH (1999) Rhodopsin's carboxy-terminal cytoplasmic tail acts as a membrane receptor for cytoplasmic dynein by binding to the dynein light chain Tctex-1. Cell 97: 877–887.
- 120. DiBella LM, Benashski SE, Tedford HW, Harrison A, Patel-King RS, et al. (2001) The Tctex1/Tctex2 class of dynein light chains. Dimerization, differential expression, and interaction with the LC8 protein family. J Biol Chem 276: 14366–14373.
- 121. Williams JC, Xie H, Hendrickson WA (2005) Crystal structure of dynein light chain TcTex-1. J Biol Chem 280: 21981–21986.
- 122. Wu H, Maciejewski MW, Takebe S, King SM (2005) Solution structure of the Tctex1 dimer reveals a mechanism for dynein-cargo interactions. Structure (Camb) 13: 213–223.
- 123. Miki F, Okazaki K, Shimanuki M, Yamamoto A, Hiraoka Y, et al. (2002) The 14-kDa dynein light chain-family protein Dlc1 is required for regular oscillatory nuclear movement and efficient recombination during meiotic prophase in fission yeast. Mol Biol Cell 13: 930–946.
- 124. Caggese C, Moschetti R, Ragone G, Barsanti P, Caizzi R (2001) Dtctex-1, the Drosophila melanogaster homolog of a putative murine t-complex distorter encoding a dynein light chain, is required for production of functional sperm. Mol Genet Genomics 265: 436–444.
- 125. Li MG, Serr M, Newman EA, Hays TS (2004) The Drosophila Tctex-1 light chain is dispensable for essential cytoplasmic dynein functions but is required during spermatid differentiation. Mol Biol Cell 15: 3005–3014.
- 126. Roux AF, Rommens J, McDowell C, Anson-Cartwright L, Bell S, et al. (1994) Identification of a gene from Xp21 with similarity to the Tctex-1 gene of the murine t complex. Hum Mol Genet 3: 257–263.
- 127. Meindl A, Dry K, Herrmann K, Manson F, Ciccodicola A, et al. (1996) A gene (RPGR) with homology to the RCC1 guanine nucleotide exchange factor is mutated in X-linked retinitis pigmentosa (RP3). Nat Genet 13: 35–42.
- 128. Douglas MW, Diefenbach RJ, Homa FL, Miranda-Saksena M, Rixon FJ, et al. (2004) Herpes simplex virus type 1 capsid protein VP26 interacts with dynein light chains RP3 and Tctex1 and plays a role in retrograde cellular transport. J Biol Chem 279: 28522–28530.
- 129. Rappold GA, Trowsdale J, Lichter P (1992) Assignment of the human homologue of the mouse t-complex gene TCTE3 to human chromosome 6q27. Genomics 13: 1337–1339.
- 130. Huw LY, Goldsborough AS, Willison K, Artzt K (1995) Tctex2: A sperm tail surface protein mapping to the t-complex. Dev Biol 170: 183–194.
- 131. Patel-King RS, Benashski SE, Harrison A, King SM (1997) A Chlamydomonas homologue of the putative murine t complex distorter Tctex-2 is an outer arm dynein light chain. J Cell Biol 137: 1081–1090.
- 132. Pazour GJ, Koutoulis A, Benashski SE, Dickert BL, Sheng H, et al. (1999) LC2, the Chlamydomonas homologue of the t complex-encoded protein Tctex2, is essential for outer dynein arm assembly. Mol Biol Cell 10: 3507–3520.
- 133. Neesen J, Drenckhahn JD, Tiede S, Burfeind P, Grzmil M, et al. (2002) Identification of the human ortholog of the t-complex-encoded protein TCTE3 and evaluation as a candidate gene for primary ciliary dyskinesia. Cytogenet Genome Res 98: 38–44.
- 134. Rappold GA, Stubbs L, Labeit S, Crkvenjakov RB, Lehrach H (1987) Identification of a testis-specific gene from the mouse t-complex next to a CpG-rich island. EMBO J 6: 1975–1980.
- 135. Bowman AB, Patel-King RS, Benashski SE, McCaffery JM, Goldstein LS, et al. (1999) Drosophila roadblock and Chlamydomonas LC7: A conserved family of dynein-associated proteins involved in axonal transport, flagellar motility, and mitosis. J Cell Biol 146: 165–180.
- 136. DiBella LM, Sakato M, Patel-King RS, Pazour GJ, King SM (2004) The LC7 light chains of Chlamydomonas flagellar dyneins interact with components required for both motor assembly and regulation. Mol Biol Cell 15: 4633–4646.
- 137. Koonin EV, Aravind L (2000) Dynein light chains of the Roadblock/LC7 group belong to an ancient protein superfamily implicated in NTPase regulation. Curr Biol 10: R774–R776.
- 138. Reuter JE, Nardine TM, Penton A, Billuart P, Scott EK, et al. (2003) A mosaic genetic screen for genes necessary for Drosophila mushroom body neuronal morphogenesis. Development 130: 1203–1213.
- 139. Pazour GJ, Witman GB (2000) Forward and reverse genetic analysis of microtubule motors in Chlamydomonas. Methods 22: 285–298.
- 140. Lunin VV, Munger C, Wagner J, Ye Z, Cygler M, et al. (2004) The structure of the MAPK scaffold, MP1, bound to its partner, p14. A complex with a critical role in endosomal map kinase signaling. J Biol Chem 279: 23422–23430.
- 141. Ye F, Zangenehpour S, Chaudhuri A (2000) Light-induced down-regulation of the rat class 1 dynein-associated protein robl/LC7-like gene in visual cortex. J Biol Chem 275: 27172–27176.
- 142. Jiang J, Yu L, Huang X, Chen X, Li D, et al. (2001) Identification of two novel human dynein light chain genes, DNLC2A and DNLC2B, and their expression changes in hepatocellular carcinoma tissues from 68 Chinese patients. Gene 281: 103–113.
- 143. Nikulina K, Patel-King RS, Takebe S, Pfister KK, King SM (2004) The roadblock light chains are ubiquitous components of cytoplasmic dynein that form homo- and heterodimers. Cell Motil Cytoskeleton 57: 233–245.
- 144. Tang Q, Staub CM, Gao G, Jin Q, Wang Z, et al. (2002) A novel transforming growth factor-beta receptor-interacting protein that is also a light chain of the motor protein dynein. Mol Biol Cell 13: 4484–4496.
- 145. Pfister KK, Fay RB, Witman GB (1982) Purification and polypeptide composition of dynein ATPases from Chlamydomonas flagella. Cell Motil 2: 525–547.
- 146. Piperno G, Luck DJ (1982) Outer and inner arm dyneins from flagella of Chlamydomonas reinhardtii. Prog Clin Biol Res 80: 95–99.
- 147. King SM, Patel-King RS (1995) The M(r) = 8,000 and 11,000 outer arm dynein light chains from Chlamydomonas flagella have cytoplasmic homologues. J Biol Chem 270: 11445–11452.
- 148. Wilson MJ, Salata MW, Susalka SJ, Pfister KK (2001) Light chains of mammalian cytoplasmic dynein: Identification and characterization of a family of LC8 light chains. Cell Motil Cytoskeleton 49: 229–240.
- 149. Naisbitt S, Valtschanoff J, Allison DW, Sala C, Kim E, et al. M (2000) Interaction of the postsynaptic density-95/guanylate kinase domain-associated protein complex with a light chain of myosin-V and dynein. J Neurosci. 20. : 4524–4534.
- 150. Yang P, Diener DR, Rosenbaum JL, Sale WS (2001) Localization of calmodulin and dynein light chain LC8 in flagellar radial spokes. J Cell Biol 153: 1315–1326.
- 151. Vadlamudi RK, Bagheri-Yarmand R, Yang Z, Balasenthil S, Nguyen D, et al. (2004) Dynein light chain 1, a p21-activated kinase 1-interacting substrate, promotes cancerous phenotypes. Cancer Cell 5: 575–585.
- 152. Espindola FS, Suter DM, Partata LB, Cao T, Wolenski JS, et al. (2000) The light chain composition of chicken brain myosin-Va: Calmodulin, myosin-II essential light chains, and 8-kDa dynein light chain/PIN. Cell Motil Cytoskeleton 47: 269–281.
- 153. Jaffrey SR, Snyder SH (1996) PIN: An associated protein inhibitor of neuronal nitric oxide synthase. Science 274: 774–777.
- 154. Puthalakath H, Huang DC, O'Reilly LA, King SM, Strasser A (1999) The proapoptotic activity of the Bcl-2 family member Bim is regulated by interaction with the dynein motor complex. Mol Cell 3: 287–296.
- 155. Schnorrer F, Bohmann K, Nusslein-Volhard C (2000) The molecular motor dynein is involved in targeting swallow and bicoid RNA to the anterior pole of Drosophila oocytes. Nat Cell Biol 2: 185–190.
- 156. Wang L, Hare M, Hays TS, Barbar E (2004) Dynein light chain LC8 promotes assembly of the coiled-coil domain of swallow protein. Biochemistry 43: 4611–4620.
- 157. Raux H, Flamand A, Blondel D (2000) Interaction of the rabies virus P protein with the LC8 dynein light chain. J Virol 74: 10212–10216.
- 158. Benashski SE, Harrison A, Patel-King RS, King SM (1997) Dimerization of the highly conserved light chain shared by dynein and myosin V. J Biol Chem 272: 20929–20935.
- 159. Liang J, Jaffrey SR, Guo W, Snyder SH, Clardy J (1999) Structure of the PIN/LC8 dimer with a bound peptide. Nat Struct Biol 6: 735–740.
- 160. Fan J, Zhang Q, Tochio H, Li M, Zhang M (2001) Structural basis of diverse sequence-dependent target recognition by the 8 kDa dynein light chain. J Mol Biol 306: 97–108.
- 161. Wu H, King SM (2003) Backbone dynamics of dynein light chains. Cell Motil Cytoskeleton 54: 267–273.
- 162. Dick T, Ray K, Salz HK, Chia W (1996) Cytoplasmic dynein (ddlc1) mutations cause morphogenetic defects and apoptotic cell death in Drosophila melanogaster. Mol Cell Biol 16: 1966–1977.
- 163. Phillis R, Statton D, Caruccio P, Murphey RK (1996) Mutations in the 8 kDa dynein light chain gene disrupt sensory axon projections in the Drosophila imaginal CNS. Development 122: 2955–2963.
- 164. Beckwith SM, Roghi CH, Liu B, Ronald MN (1998) The “8-kD” cytoplasmic dynein light chain is required for nuclear migration and for dynein heavy chain localization in Aspergillus nidulans. J Cell Biol 143: 1239–1247.
- 165. Puthalakath H, Villunger A, O'Reilly LA, Beaumont JG, Coultas L, et al. (2001) Bmf: A proapoptotic BH3-only protein regulated by interaction with the myosin V actin motor complex, activated by anoikis. Science 293: 1829–1832.
- 166. Day CL, Puthalakath H, Skea G, Strasser A, Barsukov I, et al. (2004) Localization of dynein light chains 1 and 2 and their pro-apoptotic ligands. Biochem J 377: 597–605.
- 167. Wheeler DL, Church DM, Federhen S, Lash AE, Madden TL, et al. (2003) Database resources of the National Center for Biotechnology. Nucleic Acids Res 31: 28–33.
- 168. Pruitt KD, Tatusova T, Maglott DR (2003) NCBI Reference Sequence Project: Update and current status. Nucleic Acids Res 31: 34–37.
- 169. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res 25: 3389–3402.
- 170. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215: 403–410.
- 171. Henikoff S, Henikoff JG (1993) Performance evaluation of amino acid substitution matrices. Proteins 17: 49–61.
- 172. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22: 4673–4680.
- 173. Gonnet GH, Cohen MA, Benner SA (1992) Exhaustive matching of the entire protein sequence database. Science 256: 1443–1445.
- 174. Guindon S, Gascuel O (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52: 696–704.
- 175. Ronquist F, Huelsenbeck JP (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572–1574.
- 176. Page RDM (1996) TREEVIEW: An application to display phylogenetic trees on personal computers. Comput Appl Biosci 12: 357–358.
- 177. Ahmad-Annuar A, Shah P, Hafezparast M, Hummerich H, Witherden AS, et al. (2003) No association with common Caucasian genotypes in exons 8, 13 and 14 of the human cytoplasmic dynein heavy chain gene (DNCHC1) and familial motor neuron disorders. Amyotroph Lateral Scler Other Motor Neuron Disord 4: 150–157.
- 178. Narayan D, Desai T, Banks A, Patanjali SR, Ravikumar TS, et al. (1994) Localization of the human cytoplasmic dynein heavy chain (DNECL) to 14qter by fluorescence in situ hybridization. Genomics 22: 660–661.
- 179. Nagase T, Ishikawa K, Nakajima D, Ohira M, Seki N, et al. (1997) Prediction of the coding sequences of unidentified human genes. VII. The complete sequences of 100 new cDNA clones from brain which can code for large proteins in vitro. DNA Res 4: 141–150.
- 180. Byers HR, Yaar M, Eller MS, Jalbert NL, Gilchrest BA (2000) Role of cytoplasmic dynein in melanosome transport in human melanocytes. J Invest Dermatol 114: 990–997.
- 181. Witherden AS, Hafezparast M, Nicholson SJ, Ahmad-Annuar A, Bermingham N, et al. (2002) An integrated genetic, radiation hybrid, physical and transcription map of a region of distal mouse Chromosome 12, including an imprinted locus and the “Legs at odd angles” (Loa) mutation. Gene 283: 71–82.
- 182. Fridolfsson AK, Hori T, Wintero AK, Fredholm M, Yerle M, et al. (1997) Expansion of the pig comparative map by expressed sequence tags (EST) mapping. Mamm Genome 8: 907–912.
- 183. The Jackson Laboratory (2004) Mouse Genome Database gene detail: Dync1h1(mKIAA0325 synonym). Bar Harbor (Maine): The Jackson Laboratory. Available: http://www.informatics.jax.org/searches/accession_report.cgi?id=MGI:103147. Accessed 25 November 2005.
- 184. Okazaki N, Kikuno R, Ohara R, Inamoto S, Aizawa H, et al. (2003) Prediction of the coding sequences of mouse homologues of KIAA gene: II. The complete nucleotide sequences of 400 mouse KIAA-homologous cDNAs identified by screening of terminal sequences of cDNA clones randomly sampled from size-fractionated libraries. DNA Res 10: 35–48.
- 185. Neesen J, Koehler MR, Kirschner R, Steinlein C, Kreutzberger J, et al. (1997) Identification of dynein heavy chain genes expressed in human and mouse testis: Chromosomal localization of an axonemal dynein gene. Gene 200: 193–202.
- 186. Ota T, Suzuki Y, Nishikawa T, Otsuki T, Sugiyama T, et al. (2004) Complete sequencing and characterization of 21,243 full-length human cDNAs. Nat Genet 36: 40–45.
- 187. The Jackson Laboratory (2004) Mouse Genome Database, Mouse Genome Informatics Web site. Bar Harbor (Maine): The Jackson Laboratory. Available: http://www.informatics.jax.org. Accessed 25 November 2005. Version 3.0 retrieved March 2004.
- 188. National Center for Biotechnology Information (1998) Homo sapiens cDNA clone MPMGp800I08506 5' similar to DYNEIN INTERMEDIATE CHAIN 1. Bethesda (Maryland): National Center for Biotechnology Information. Available: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=31744556&txt=on. Accessed 25 November 2005.
- 189. National Center for Biotechnology Information (1998) Homo sapiens cDNA clone MPMGp800C22508 5' similar to DYNEIN INTERMEDIATE CHAIN 2. Bethesda (Maryland): National Center for Biotechnology Information. Available: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=31743626&txt=on. Accessed 25 November 2005.
- 190. National Center for Biotechnology Information (2004) Entrez Gene DNC1LI1 LocusLink entry: Dynein Light Chain A synonym. Bethesda (Maryland): National Center for Biotechnology Information. Available: http://www.ncbi.nlm.nih.gov/LocusLink/LocRpt.cgi?l=51143. Accessed 25 November 2005.
- 191. National Center for Biotechnology Information (2004) Entrez Nucleotide database Dync1li1 entry: MGC32416 synonym. Bethesda (Maryland): National Center for Biotechnology Information. Available: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=22122794. Accessed 25 November 2005.
- 192. National Center for Biotechnology Information (2004) Entrez Nucleotide database DYNC2LI1 entry: D2LIC, LIC3, CGI-60, DKFZP564A033 synonyms. Bethesda (Maryland): National Center for Biotechnology Information. Available: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=40548412. Accessed 25 November 2005.
- 193. National Center for Biotechnology Information (2004) Entrez Nucleotide database mouse Dync2li1 entry: D2LIC, mD2LIC, MGC7211, MGC40646, 4933404O11Rik synonyms. Bethesda (Maryland): National Center for Biotechnology Information. Available: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=26986540. Accessed 25 November 2005.
- 194. Watanabe TK, Fujiwara T, Shimizu F, Okuno S, Suzuki M, et al. (1996) Cloning, expression, and mapping of TCTEL1, a putative human homologue of murine Tcte1, to 6q. Cytogenet Cell Genet 73: 153–156.
- 195. Mueller S, Cao X, Welker R, Wimmer E (2002) Interaction of the poliovirus receptor CD155 with the dynein light chain Tctex-1 and its implication for poliovirus pathogenesis. J Biol Chem 277: 7897–7904.
- 196. Shibata K, Itoh M, Aizawa K, Nagaoka S, Sasaki N, et al. (2000) RIKEN integrated sequence analysis (RISA) system—384-format sequencing pipeline with 384 multicapillary sequencer. Genome Res 10: 1757–1771.
- 197. National Center for Biotechnology Information (2004) DNCL2A GenBank entry: MGC15113 synonym. Bethesda (Maryland): National Center for Biotechnology Information. Available: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?29570778:NCBI:5998190. Accessed 25 November 2005.
- 198. Dole V, Jakubzik CR, Brunjes B, Kreimer G (2000) A cDNA from the green alga Spermatozopsis similis encodes a protein with homology to the newly discovered Roadblock/LC7 family of dynein-associated proteins. Biochim Biophys Acta 1490: 125–130.
- 199. Fracchiolla NS, Cortelezzi A, Lambertenghi-Deliliers G (1999) BitH, a human homolog of bithorax Drosophila melanogaster gene, on Chromosome 20q. Available: EMBL Nucleotide Sequence Database (http://www.ebi.ac.uk/embl), GenBank (http://www.ncbi.nlm.nih.gov/Genbank), and DNA Data Bank of Japan (DDBJ) (http://www.ddbj.nig.ac.jp) databases. Accessed 25 November 2005.
- 200. Quackenbush J, Cho J, Lee D, Liang F, Holt I, et al. (2001) The TIGR gene indices: Analysis of gene transcript sequences in highly sampled eukaryotic species. Nucleic Acids Res 29: 159–164.
- 201. Zhang QH, Ye M, Wu XY, Ren SX, Zhao M, et al. (2000) Cloning and functional analysis of cDNAs with open reading frames for 300 previously undefined genes expressed in CD34+ hematopoietic stem/progenitor cells. Genome Res 10: 1546–1560.
- 202. Cras-Meneur C, Inoue H, Zhou Y, Ohsugi M, Bernal-Mizrachi E, et al. (2004) An expression profile of human pancreatic islet mRNAs by serial analysis of gene expression (SAGE). Diabetologia 47: 284–299.
- 203. Crepieux P, Kwon H, Leclerc N, Spencer W, Richard S, et al. (1997) I kappaB alpha physically interacts with a cytoskeleton-associated protein through its signal response domain. Mol Cell Biol 17: 7375–7385.
- 204. National Center for Biotechnology Information (2004) GenBank DlC2 entry: MGC17810 synonym. Bethesda (Maryland): National Center for Biotechnology Information. Available: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=18087854. Accessed 25 November 2005.
- 205. National Center for Biotechnology Information (2004) GenBank Dlc2 entry: 6720463E02Rik and 1700064A15Rik synonym. Bethesda (Maryland): National Center for Biotechnology Information. Available: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=31542030. Accessed 25 November 2005.
- 206. Strausberg RL, Feingold EA, Grouse LH, Derge JG, Klausner RD, et al. (2002) Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Proc Natl Acad Sci U S A 99: 16899–16903.
- 207. Lai CH, Chou CY, Ch'ang LY, Liu CS, Lin Wc (2000) Identification of novel human genes evolutionarily conserved in Caenorhabditis elegans by comparative proteomics. Genome Res 10: 703–713.
- 208. Tajima F (1983) Evolutionary relationship of DNA sequences in finite populations. Genetics 105: 437–460.
- 209. Pamilo P, Nei M (1988) Relationships between gene trees and species trees. Mol Biol Evol 5: 568–583.
- 210. Pfister KK, Fisher EM, Gibbons IR, Hays TS, Holzbaur EL, et al. (2005) Cytoplasmic dynein nomenclature. J Cell Biol 171: 411–413.