The assembly and motility of eukaryotic cilia and flagella require the action of a large array of dynein microtubule motor complexes. These enzymes display distinct motile properties (
Kagami and Kamiya, 1992;
Moss et al., 1992a;
Moss et al., 1992b;
Sakakibara and Nakayama, 1998) and contain one or more heavy chain(s) (HCs
1; ~500 kDa) that exhibit ATPase and microtubule motor activity. In addition, the dynein HCs are associated with a complex array of smaller polypeptides that are necessary for motor assembly, regulation, and attachment to the appropriate cargo {reviewed in (
King and Kamiya, 2009)}. Due to the ease of genetic and biochemical analyses, a cell architecture that allows clear observation of flagellar movement, and a sequenced genome (
Merchant et al., 2007), the biflagellate green alga
Chlamydomonas reinhardtii has become the premier model system in which to dissect the role of dyneins in axoneme-based motility and in the assembly of cilia/flagella.
Chlamydomonas expresses sixteen dynein HCs that form a series of motor complexes with different functions. The outer dynein arm, containing three distinct HCs, is required for high power output by the flagellum (
Piperno and Luck, 1979;
Pfister et al., 1982;
Brokaw, 1999). Two different general types of inner dynein arms, one containing a HC heterodimer and a second consisting of monomeric HC species, are needed to define the waveform (
Brokaw and Kamiya, 1987;
Kamiya et al., 1991) and/or for beating under high viscous load (
Yagi et al., 2005). Finally, a homodimeric dynein (here termed the IFT dynein) powers retrograde intraflagellar transport (IFT) and is thus necessary for assembly and maintenance of the organelle (
Pazour et al., 1999;
Porter et al., 1999). Although
C. reinhardtii contains a large complement of flagellar dyneins, its genome does not encode most of the components comprising the conventional
cytoplasmic dynein 1/dynactin system that in other organisms (such as mammals) is required for a wide array of microtubule-based intracellular transport activities (
Pfister et al., 2006;
Merchant et al., 2007;
Wickstead and Gull, 2007); the exceptions are certain light chains (LCs) employed by both conventional cytoplasmic dynein and other dynein subtypes (
King et al., 1996;
Harrison et al., 1998;
Bowman et al., 1999).
To date, a total of fifty-four gene products have been identified in
C. reinhardtii as integral components of these dynein motors or as factors required for their assembly in the cytoplasm, transport into the flagellum, and/or localization within the axonemal superstructure {see (
Cole, 2009;
King and Kamiya, 2009) for reviews}. These proteins have been identified by numerous laboratories over many years utilizing a variety of methods including genetic analysis of mutants with defective flagella, direct protein biochemistry and, more recently, comparative genomic approaches. As a result, the genes, their encoded proteins and mutant strains have been given a wide variety of names derived from various nomenclature schemes. The resulting plethora of terms and aliases has become unwieldy and complicated. Moreover, the nomenclature of the orthologous dynein components in other species is often quite distinct from that used in
C. reinhardtii, and this continues to engender considerable confusion in the literature, and in some cases has led to the misidentification of gene products.
Historically, this general problem derives, at least in part, from the fact that many
C. reinhardtii, sea urchin
2 and
Tetrahymena thermophila dynein proteins were given alphanumeric assignments based on the order of their migration in SDS and/or urea polyacrylamide gels many years before any of the sequences were known. Thus, differences in migration patterns due to minor variations in size, sequence and/or charge resulted in orthologous proteins being given completely different designations. Unfortunately, the issue was compounded during annotation of the mouse and human genomes when certain dynein genes were named after their
C. reinhardtii counterparts whereas others followed the sea urchin protein nomenclature. For example, mammalian DNAL4 was named after the LC4 component of the sea urchin outer arm dynein which is orthologous to
C. reinhardtii LC10; confusingly, in
C. reinhardtii LC4 denotes a calmodulin homologue and thus a member of a completely unrelated protein family. Conversely, mammalian DNAL1 was named after the
C. reinhardtii outer arm dynein leucine- rich repeat protein LC1 (the sea urchin orthologue of which is termed LC2 in one nomenclature scheme), whereas sea urchin LC1 is a member of the Tctex1/Tctex2 protein family. This level of confusion also extends to the HCs where, for example, the gene for the 1α HC of inner arm dynein I1/f is
DHC1 in
C. reinhardtii, DNAH10 in sea urchins and mammals and
DYH6 in
T. thermophila, while the 1β HC of that same dynein is termed
DHC10 (
C. reinhardtii),
DNAH2 (sea urchins and mammals) and
DYH7 (
T. thermophila).
Given the long history of these names in dynein research combined with the complexity of the gene families and the large variety of organisms involved, there seems to be no way of synthesizing a gene nomenclature/numbering scheme that is completely consistent across a broad phylogenetic spectrum and incorporates all the major model organisms while still maintaining continuity with the older literature. Consequently, as part of a re-annotation effort for the C. reinhardtii genome, we describe in this report a new consensus nomenclature for dynein genes in C. reinhardtii. Furthermore, we provide a series of tables that indicate i) the various gene aliases, and mutant and protein names that have been used in C. reinhardtii, and ii) the identity of the orthologous components in a variety of other model organisms where that correspondence can be unambiguously defined.
The publisher's final edited version of this article is available at 
Protein Aliases,