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Logo of nihpaAbout Author manuscriptsSubmit a manuscriptHHS Public Access; Author Manuscript; Accepted for publication in peer reviewed journal;
 
Cytoskeleton (Hoboken). Author manuscript; available in PMC 2012 October 1.
Published in final edited form as:
PMCID: PMC3222151
NIHMSID: NIHMS336176

A Unified Taxonomy for Ciliary Dyneins

Abstract

The formation and function of eukaryotic cilia/flagella require the action of a large array of dynein microtubule motor complexes. Due to genetic, biochemical, and microscopic tractability, Chlamydomonas reinhardtii has become the premier model system in which to dissect the role of dyneins in flagellar assembly, motility, and signaling. Currently, fifty-four proteins have been described as components of various Chlamydomonas flagellar dyneins or as factors required for their assembly in the cytoplasm and/or transport into the flagellum; orthologues of nearly all these components are present in other ciliated organisms including humans. For historical reasons, the nomenclature of these diverse dynein components and their corresponding genes, mutant alleles and orthologues has become extraordinarily confusing. Here, we unify Chlamydomonas dynein gene nomenclature and establish a systematic classification scheme based on structural properties of the encoded proteins. Furthermore, we provide detailed tabulations of the various mutant alleles and protein aliases that have been used and explicitly define the correspondence with orthologous components in other model organisms and humans.

Keywords: Chlamydomonas, Cilia, Dynein, Flagella, Microtubule

Introduction

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) (HCs1; ~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 urchin2 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 Nomenclature

Here we propose new names for the C. reinhardtii dynein genes. The formal standard for gene names in C. reinhardtii is a three-letter root (all capitals) followed by a number (Dutcher and Harris, 1998). As the dynein genes encode a wide range of protein structural and functional types, we have employed these features, as far as possible, to form the basis of the new nomenclature. A list of the proposed dynein gene roots and their derivation is provided in Table 1. The assignment of new gene names, the older gene indicator(s) used in previous annotations of the C. reinhardtii genome, the accession number and the encoded protein products are tabulated in Table 2. Whenever possible, the proposed gene names are based on previous names; e.g. DHC1-DHC11 are unchanged. The nomenclature scheme also provides a rational basis for the naming of new genes encoding dynein subunits as these are identified; we propose these be numbered sequentially.

Table 1
Proposed Roots for C. reinhardtii Dynein Genes
Table 2
C. reinhardtii Dynein Gene Nomenclature

It is important to note that although we propose altering the gene names to yield an internally consistent scheme, we suggest that current mutant and protein names be retained so as to maintain continuity in the literature. Thus, we recommend that when describing a gene product in a publication, the corresponding gene name be used at first mention so that the gene product is unambiguously identified, and that the common protein and/or mutant names be employed thereafter. This could be readily achieved by inclusion of a brief statement such as “DHC1b (encoded at DHC16) is the dynein motor subunit responsible for retrograde IFT”.

Mutants, Protein Aliases, and Orthologues

Mutants defective in dynein genes have been identified through a variety of genetic screens following UV or insertional mutagenesis. These strains exhibit a range of phenotypes including various degrees of flagellar dysfunction, slow swimming, and impaired flagellar assembly depending on the mutant allele and the particular component that is altered. For example, strains unable to assemble outer dynein arms exhibit a characteristic slow, jerky swimming phenotype (Kamiya and Okamoto, 1985; Mitchell and Rosenbaum, 1985), whereas those with defective inner arms have defects in forming bends of appropriate amplitude (Kamiya et al., 1991). The mutant alleles that have been isolated for each component and the various aliases used for the encoded proteins are listed in Table 3.

Table 3
Nomenclature of C. reinhardtii Dynein Proteins and Representative Mutant Alleles

As detailed above, much confusion has built up in the literature about which dynein components are orthologous due to the long history of dynein research and the multiple naming schemes used in various organisms. Consequently, Table 4 provides a listing of the current C. reinhardtii gene and protein names along with their orthologues (where those can be unambiguously determined) in the ciliate T. thermophila, the sea urchins Anthocidaris crassispina and Strongylocentrotus purpuratus, the primitive chordate Ciona intestinalis, the fish Danio rerio, and the mammal Homo sapiens. A more comprehensive tabulation is provided in the supplemental table available on-line.

Table 4
Nomenclature of Orthologous Ciliary/Flagellar Dynein Components**

In conclusion, we describe here a new consensus nomenclature for the flagellar dynein genes of C. reinhardtii and provide a comprehensive tabulation of the gene products and various aliases, the mutant alleles isolated for each gene, and the designations of orthologous components in other model organisms. Axonemal dyneins provide the basis for ciliary motion in all organisms with motile cilia, and IFT dynein is necessary for the assembly and maintenance of cilia in most ciliated organisms. Because of its utility for biochemical and genetic analyses, C. reinhardtii has been a favorite model for understanding the composition and function of these flagellar dyneins. As research on dynein advances in C. reinhardtii and other model organisms with their own advantages, the nomenclature proposed here will provide a logical basis for the naming of newly identified dynein genes and mutant alleles and facilitate comparisons between C. reinhardtii and the other organisms. Finally, defects in subunits of both IFT dynein and axonemal dyneins are known to result in human disease (Dagoneau et al., 2009; Escudier et al., 2009; Leigh et al., 2009; Merrill et al., 2009), and the homologous relationships between C. reinhardtii and H. sapiens genes clarified here should expedite identification and analysis of candidate disease genes in human patients.

Methods

The Chlamydomonas dynein genes identified here are the result of a C. reinhardtii genome re- annotation initiative (Hom et al., in preparation), based on models generated using the gene- calling program AUGUSTUS (Stanke et al., 2008). Proteome datasets (sources given in Supplementary Table S1) for Tetrahymena thermophila C3, Trypanosoma brucei TREU 927, Strongylocentrotus purpuratus (sea urchin), Ciona intestinalis (sea squirt), Drosophila melanogaster (fruit fly), Danio rerio (zebra fish), and Homo sapiens (human) were pair-wise aligned to the set of C. reinhardtii dyneins by context-specific BLAST (Biegert and Soeding, 2009). Hits with bit scores within 2% of the best hit were collected and orthologues were assigned by manual inspection, mindful of the analyses by Wickstead and Gull (2007) and Wilkes et al. (2008). Hits to multiple C. reinhardtii dynein genes were treated conservatively: when one-to-one orthologue associations were uncertain, homologous proteins were grouped into sub-classes.

Supplementary Material

Supp Table S1

Acknowledgements

Our laboratories are supported by National Institutes of Health grants GM032843 (to SKD), GM044228 (to DRM), GM060992 (to GJP), GM055667 (to MEP), GM51173 (to WSS), GM030626 (to GBW) and GM051293 (to SMK), and by the Robert W. Booth Endowment (to GBW), a Grant-in-Aid for Scientific Research (C) from MEXT (to TY), and a grant from the Ministry of Education, Culture, Sports and Technology of Japan (to RK). MW is supported by grants to WSS from the National Institutes of Health (GM051173) and the National Institute on Alcohol Abuse and Alcoholism (P50-AA-13575). EFYH was supported in part by the Jane Coffin Childs Memorial Research Fund and the NIGMS Center for Systems Biology (GM068763).

Footnotes

1Abbreviations used: DC, docking complex; HC, heavy chain; IC, intermediate chain; IFT, intraflagellar transport; LC, light chain; LIC, light intermediate chain; LRR, leucine-rich repeat; NDK, nucleoside diphosphate kinase.

2Multiple species of sea urchin have been used for biochemical studies by different laboratories depending on geographic and seasonal variables. The most commonly employed include: Anthocidaris crassispina, Arbacia punctulata, Hemicentrotus pulcherrimus, Lytechinus pictus, Pseudocentrotus depressus, Strongylocentrotus droebachiensis, Strongylocentrotus purpuratus, and Tripneustes gratilla.

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