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.

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

Gene Family Root	Root Derivation	Characteristics of Protein Family
DHC	Dynein Heavy Chain	ATPases / Motors
DIC	Dynein Intermediate Chain	WD-repeat proteins
DLI	Dynein Light Intermediate chain	Originally named based on migration between ICs and LCs. Class found only in “cytoplasmic” dyneins, including IFT dynein
DLU	Dynein components with LeUcine-rich repeats	Contain ββα barrels derived from leucine-rich repeats
DLX	Dynein Light chain thioredoXin	Redox-sensitive thioredoxins with vicinal dithiols
DLT	Dynein Light chain Tctex1-like	Tctex1/Tctex2 family proteins; some are also found in conventional cytoplasmic dynein
DLR	Dynein Light chain Roadblock-like	Related to the Roadblock light chains found in conventional cytoplasmic dynein
DLL	Dynein Light chain in LC8 family	Very highly conserved family of dimeric light chains found in many enzyme systems
DLE	Dynein Light chain in EF-hand family	Ca2+-binding components containing EF-hand motif(s)
DCC	Dynein Coiled Coil	Contain extensive regions of coiled -coil structure
DOI	Dynein Outer arm-Interacting	Associate with outer arm dynein but do not fall into other categories
DII	Dynein Inner arm-Interacting	Associate with inner arm dyneins but do not fall into other categories
DAP	Dynein Assembly PIH domain	Required for dynein assembly and contain PIH domains
DAW	Dynein Assembly WD repeat	Required for dynein assembly and contain WD-repeat motifs
DAU	Dynein Assembly leUcine-rich repeat	Required for dynein assembly and contain leucine-rich repeat motifs
DAB	Dynein Assembly Blocked	Required for dynein assembly but do not fall into other categories

Table 2.

C. reinhardtii Dynein Gene Nomenclature^‡

Heavy Chains
DHC1	DHC1(IDA1, PF9)	Q9SMH3	1α heavy chain of inner arm I1/f
DHC2	DHC2	XP_001694660	Inner arm dynein species d heavy chain
DHC3	DHC3	XP_001696272	Inner arm dynein heavy chain (minor species) †
DHC4	DHC4	EDP07657	Inner arm dynein heavy chain (minor species) †
DHC5	DHC5	XP_001699742	Inner arm dynein species b heavy chain
DHC6	DHC6	XP_001700741	Inner arm dynein species a heavy chain
DHC7	DHC7	XP_001692695	Inner arm dynein species g heavy chain
DHC8	DHC8	XP_001692092	Inner arm dynein species e heavy chain
DHC9	DHC9(IDA9)	BAE19786	Inner arm dynein species c heavy chain
DHC10	DHC10(IDA2)	Q9MBF8	1β heavy chain of inner arm I1/f
DHC11	DHC11	XP_001694047	Inner arm dynein heavy chain (minor species) †
DHC12	DHC1a (PCR4)	EDP05194	Inner arm dynein heavy chain#
DHC13	ODA11	Q39610	α outer arm heavy chain
DHC14	ODA4	Q39565	β outer arm heavy chain
DHC15	ODA2	Q39575	γ outer arm heavy chain
DHC16	DHC1b	Q9SMH5	dynein heavy chain that mediates retrograde IFT
WD-repeat Intermediate Chains
DIC1	ODA9	Q39578	IC1 from outer arm dynein
DIC2	ODA6	P27766	IC2 from outer arm dynein
DIC3	IDA7	AAD45352	IC140 from inner arm I1/f dynein
DIC4	BOP5	AAU93505	IC138 from inner arm I1/f dynein
DIC5	FAP133	XM_001699649	IFT dynein intermediate chain
Light Intermediate Chains
DLI1	D1bLIC	AAT37069	Light intermediate chain of IFT dynein
Leucine-rich repeat Proteins
DLU1	LC1(DLC1)	AAD41040	Outer arm dynein γ heavy chain- associated
DLU2	ODA8(MOT37)	EPD09919	ODA8 protein required for outer arm assembly
Thioredoxin-like Light Chains
DLX1	LC3(DLC3)	Q39592	LC3 thioredoxin associated with outer arm β heavy chain
DLX2	LC5(DLC5)	Q39591	LC5 thioredoxin associated with outer arm α heavy chain
Tctex1-like Light Chains
DLT1	LC9 *	AAZ95589	LC9 present in outer arm dynein
DLT2	ODA12	AAB58383	LC2 present in outer arm dynein
DLT3	TCTEX1	AAC18035	Tctex1 present in inner arm I1/f
DLT4	TCTEX2b	DAA05278	Tctex2b present in inner arm I1/f
Roadblock-like Light Chains
DLR1	ODA15(DLC7a)	AAD45881	LC7a present in outer arm and inner arm I1/f dyneins
DLR2	LC7b(DLC7b)	EDP03034	LC7b present in outer arm and inner arm I1/f dyneins
DYNLL/LC8 Family Light Chains
DLL1	FLA14	Q39580	LC8 present in outer arm, inner arm I1/f and IFT dyneins. Also a component of the radial spokes
DLL2	ODA13	Q39579	Outer arm dynein LC6
DLL3	LC10(MOT24)	EDP00562	Outer arm dynein LC10
Calmodulin Homologues
DLE1	LC4(DLC4)	Q39584	LC4 present in outer arm dynein. Binds Ca2+
DLE2	VFL2	P05434	Centrin present in monomeric inner arm dyneins b, e and g. This gene is also termed CNT1 (named for CeNTrin). Binds Ca2+
DLE3	ODA14	AAP49435	DC3 component of outer arm docking complex. Binds Ca2+
Coiled Coil Proteins
DCC1	ODA3	AAC49732	DC1 of the outer arm docking complex
DCC2	ODA1	AAK72125	DC2 of the outer arm docking complex
DCC3	ODA5 *	AAS10183	Oda5 protein that associates with an adenylate kinase
Outer Arm Dynein Interacting Proteins
DOI1	LIS1*	ABG33844	Lis1 protein associates with α heavy chain of outer arm
Inner Arm Dynein Interacting Proteins
DII1	IDA4	Q39604	p28 light chain present in inner arm species a, c and d
DII2	FAP146	BAG07147	p38 associates with inner arm species d
DII3	*	BAF98914	p44 associates with inner arm species d
DII4	IDA5	P53498	Actin, present in inner arm dynein species a, b, c, d, e, g and some minor species. This gene is also known as ACT1 (named for ACTin)
DII5	NAP1	AAC49834	NAP, novel actin-related protein that can substitute for actin in inner arm dyneins b and g. This gene is also known as ARP12 (named for Actin Related Protein).
DII6	FAP94	EDP03678	IC97 present in inner arm I1/f dynein
DII7	FAP120	EDP07339	Ankyrin-repeat protein that interacts with IC138(DIC4) from inner arm I1/f
Dynein Assembly Proteins Containing a PIH Domain
DAP1	PF13 (MOT45)	BAG69288	PF13 protein required for inner/outer arm assembly in cytoplasm
DAP2	IDA10 (MOT48)	BAI83444	MOT48 protein required for inner arm assembly in cytoplasm¶
Dynein Assembly Proteins containing WD Repeats
DAW1	ODA16	AAZ77789	ODA16 protein acts as an IFT adaptor for outer arm dynein
Dynein Assembly Proteins containing Leucine-rich Repeats
DAU1	ODA7	Q09JZ4	ODA7 is a LRR protein required for outer arm assembly in cytoplasm
Dynein Assembly Blocked
DAB1	PF22	AEC04845	PF22 is required for assembly of outer arms

^‡Alternative gene names are indicated in parentheses in the first two columns.

^*These genes were missing and/or not named in the Chlamydomonas version 3 genome catalogue.

^#T. Yagi (unpublished results).

^†Yagi et al. (2009)

^¶Yamamoto et al. (2010)

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

Gene Name	Mutant Alleles	Protein Aliases*
DHC1	ida1-1 → ida1-6, pf9-1 → pf9-4, pf30	1α HC
DHC2	----	DHC2
DHC3	----	DHC3
DHC4	----	DHC4
DHC5	----	DHC5
DHC6	----	DHC6
DHC7	----	DHC7
DHC8	----	DHC8
DHC9	ida9	DHC9
DHC10	ida2-1 → ida2-6	1β HC
DHC11	----	DHC11
DHC12	----	DHC12
DHC13	oda11	αHC
DHC14	oda4-1 → oda4-4, oda4-s7, suppf1-1, suppf1-2	βHC
DHC15	oda2, oda2-t, pf28, suppf2	γHC
DHC16	dhc1b-1, stf1-1, stf1-2, dhc1b-2 (=dhc1bts)	DHC1b
DIC1	oda9-1, oda9-2(V5), oda9-3(V8), oda9-4(V24), oda9-5(V27)	IC1, IC78, IC80, Mr78,000
DIC2	oda6-1, oda6-2, oda6-r75, oda6-r88	IC2, IC69, IC70, Mr69,000
DIC3	ida7	IC140, Mr140,000
DIC4	bop5-1, bop5-2	IC138, Mr138,000
DIC5	----	D1bIC, FAP133
DLI1	d1blic, d1blic::D1bLIC(K53S), d1blic::D1bLIC(K53I, S54A)	D1bLIC, LIC
DLU1	----	LC1, Mr22,000
DLU2	oda8-1 → oda8-3	ODA8
DLX1	----	LC3, Mr16,000
DLX2	----	LC5, Mr14,000
DLT1	----	LC9
DLT2	oda12-1†, oda12-2	LC2, Mr19,000
DLT3	----	Tctex1
DLT4	pf16(D2) ‡	Tctex2b
DLR1	oda15	LC7a, LC7
DLR2	----	LC7b
DLL1	fla14-1, fla14-2	LC8, Mr8,000, 8 kDa
DLL2	oda13	LC6, Mr11,000
DLL3	oda12-1f †	LC10, MOT24
DLE1	----	LC4, Mr18,000
DLE2(CNT1)	vfl2-1, vfl2-R1, vfl2-R5, vfl2-R8, vfl2-R10, vfl2-R11, vfl2-R13	Centrin
DLE3	oda14-1(V06), oda14-2(V16), oda14- 3(F28)+, oda14-1::ODA14(E74Q, E152Q)	DC3
DCC1	oda3-1, oda3-2, oda3-4, oda3-5	DC1
DCC2	oda1-1 → oda1-3	DC2
DCC3	oda5-1, oda5-2	ODA5
DOI1	----	LIS1
DII1	ida4-1 → ida4-3	p28
DII2	----	p38
DII3	----	p44
DII4 (ACT1)	ida5	actin
DII5 (ARP12)	----	NAP
DII6	----	IC97,IC110
DII7	----	FAP120
DAP1	pf13-1, pf13-2 (pf13A), pf13-3	PF13
DAP2	ida10, mot48	MOT48
DAW1	oda16	ODA16
DAU1	oda7	ODA7
DAB1§	pf22-1, pf22-2(pf22A)	PF22

^*The current preferred protein name is indicated first in bold type.

^†The DLT2 and DLL3 genes are adjacent; both are completely deleted in oda12-1.

^‡pf16(D2) lacks both the DLT4 and PF16 genes; the latter encodes a component of the central pair microtubule complex.

⁺The oda14-3(F28) allele also lacks the RSP14 gene which encodes a component of the radial spokes.

^§The DAB1 gene is currently missing from the version 4 genome assembly.

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^{** †}

	C. reinhardtii		T. thermophila	A. crassispina & S. purpuratus**	Ci. intestinalis	D. rerio	H. sapiens
Heavy Chains	Gene	Protein	Gene (Protein)	Protein	Protein	Gene	Gene
Inner Arm I1/f	DHC1	1α HC	DYH6	DNAH10			DNAH10
	DHC10	1β HC	DYH7	DNAH2			DNAH2
	DHC13	α HC	DYH5 (γ HC)	----	----		----
	DHC14	β HC	DYH4 (β HC)	β HC (Sp-DNAH9)	α HC		DNAH9
Outer Arm							DNAH11 DNAH17
	DHC15	γ HC	DYH3 (α HC)	α HC (Sp-DNAH5, Sp-DNAH8, Sp- DNAH15)	β HC		DNAH5 DNAH8
IFT Dynein†	DHC16	DHC1b	DYH2	Sp-DYNC2H1		Dync2h1	DYNC2H1
	DHC4	DHC4	DYH8	DNAH3		DNAH7	DNAH3
	DHC5	DHC5	DYH10	DNAH4		DNAH12	DNAH7
Inner Arm Group 3	DHC6	DHC6	DYH12	DNAH7			DNAH12
	DHC8	DHC8	DYH13	DNAH12			DNAH14
	DHC9	DHC9	DYH14
	DHC11	DHC11	DYH17 DYH18 DYH25
	DHC2	DHC2	DYH9	DNAH1			DNAH1
Inner Arm Group 4			DYH11 DYH16 DYH19 DYH20				DNAH6
	DHC3	DHC3	DYH15	DNAH6
Inner Arm Group 5	DHC7	DHC7	DYH22 DYH23 DYH24
Un- assigned	DHC12	DHC12
Inter- mediate Chains	----	----	----	IC1$	IC3$		TXNDC3 $ (Sptrx2)
Outer Arm	DIC1	IC1	IC2	IC2 (Sp-DNAI1)	IC2		DNAI1
	DIC2	IC2	IC3	IC3 (Sp-DNAI2)	IC1		DNAI2
Inner Arm	DIC3	IC140	IC5				WDR63
	DIC4	IC138	IC6			Wdr78	WDR78
IFT Dynein	DIC5	D1bIC	D2IC			Dync2i1	WDR34
Light Inter- mediate Chain†	DLI1	D1bLIC	D2LIC	D2LIC (Sp- DYNC2LI1)		Dync2li1	DYNC2LI1
Light Chains	DLU1	LC1	LC1	LC2 (Sp-DNAL1)	LC1		DNAL1
	DLU2	ODA8		LRRC56			LRRC56
	DLX1	LC3	LC3A (LC3-like A) LC3B (LC3-like B)	----		----	----
	DLX2	LC5		----	----	----	----
	DLT1	LC9	TCT1A (Tctex1A)	LC3 (Sp-DYNLT1)	LC3		DYNLT1 *
	DLT3	Tctex1	TCT1B (Tctex1B)				(Tctex1) DYNLT3 (rp3)
	DLT2	LC2	LC2A	LC1 (Sp-DYNLT2)	LC2		TCTE3 (Tctex2)
	DLT4	Tctex2b	LC2B
	DLR1	LC7a	LC7A	RBPH (Sp-DYNLRB1)	LC5		DYNLRB1 *
	DLR2	LC7b	LC7B	LC7L1 (Sp-DYNLRB2)			DYNLRB2
	DLL1	LC8	LC8n ††	LC6 (Sp-DYNLL1)	LC6		DYNLL1 DYNLL2
	DLL2	LC6	LC8x (LC8-like) ††	----			----
	DLL3	LC10	LC10	LC4 (Sp-DNAL4)	LC4		DNAL4
	DLE1	LC4	LC4A LC4B	----			----
	DLE2 (CNT1)	centrin	CEN1 (centrin)				CETN1, CETN2, CETN3
	DLE3	DC3
Other Compon- ents	DCC1	DC1			IC4
	DCC2	DC2			IC5, Axp66.0		CCDC114
	DCC3	ODA5					CCDC63
	DOI1	LIS1
	DII1	p28	p28A p28B p28C	p33 (Sp-DNALI1)			DNALI1
	DII2	p38		ZMYND12			ZMYND12
	DII3	p44		TTC29			TTC28
	DII4 (ACT1)	actin	ACT1 (actin)	actin¶	actin¶	actin ¶	actin ¶
	DII5 (ARP1)	NAP
	DII6	FAP94		CASC1			CASC1
	DII7	FAP120
Assembly Factors	DAP1	PF13				Kintoun #	DNAAF2
	DAP2	MOT48		PIH1D1		Pih1d1	PIH1D1
	DAW1	ODA16		WDR69		Wdr69	WDR69
	DAU1	ODA7		LRRC50		Lrrc50	DNAAF1 (LRRC50)
	DAB1	PF22

^**Initial biochemical identification of proteins comprising the axonemal dyneins of various model organisms was reported by multiple groups including: for C. reinhardtii, Pfister et al. (1982), Piperno and Luck (1979); for the sea urchin Tripneustes gratilla, Bell et al. (1979); for T. thermophila, Porter and Johnson (1983); and for Ci. intestinalis, Hozumi et al (2006).

^‡This table illustrates the names of orthologous components where that can be unambiguously determined. In some cases, multiple proteins in one organism are more closely related to each other than they are to any proteins present in another organism. Thus, for the monomeric inner arm HCs (and some other components), phylogenetic analysis does not provide for a clear correspondence at the level of individual proteins. However, subgroupings are more clear (see also Wickstead and Gull, 2007 and Wilkes et al., 2008) and are indicated here, although it is important to note that some ambiguity still remains.

^§There are at least two nomenclatures for sea urchin axonemal dynein components currently in use. One derives from the original protein biochemistry and early sequence analysis of outer arm dynein components performed by a number of laboratories most notably those of Ian Gibbons (e.g. Bell et al., 1979) and Kazuo Ogawa (e.g. Ogawa et al., 1996, and light chain sequences published only in the database). More recent annotation of the S. purpuratus genome identified additional components of sea urchin dyneins and provided alternate names for some components based mainly on the scheme used in mammals (Morris et al., 2006).

^†The IFT dynein subunits in the nematode Caenorhabditis elegans are known as CHE3 (heavy chain), XBX-1 (light intermediate chain), and XBX-2 (a Tctex1/Tctex2 family light chain). A dynein IC involved in IFT has not yet been unambiguously identified in Ca. elegans. Ca. elegans lacks axonemal dyneins.

^$These ICs are modular proteins consisting of an N-terminal thioredoxin domain followed by several catalytic nucleoside diphosphate kinase (NDK) modules. The N-terminal domain is closely related to C. reinhardtii LC3 (DLX1) and LC5 (DLX2). However, subunits of the C. reinhardtii outer arm do not contain the NDK modules.

^*Mammals express two canonical Tctex1 proteins (DYNLT1 and DYNLT3) and two DYNLRB proteins. It remains uncertain which members of these groups are orthologous to the C. reinhardtii flagellar dynein components. Thus, both members of each group are listed.

^††The analysis of Wilkes et al. (2007) recognized LC8 and five LC8-like sequences (ABF38951-ABF38955) in T. thermophila; LC8D (LC8-likeD) (ABF38954) appeared most closely related to C. reinhardtii LC6 (DLL2), although our analysis suggest this assignment is ambiguous with respect to other LC8-like sequences, notably LC8C (ABF38953). Furthermore, none of these T. thermophila LC8-like sequences contain the loop region insert that characterizes C. reinhardtii LC6. The most recent T. thermophila genome release includes only canonical LC8 and LC8E (LC8-likeE) genes. As amino acid differences occur throughout the LC8-likeA - LC8-likeE sequences, these sequences are unlikely to be generated by alternative splicing. It is possible that the current genome assembly has erroneously combined these genes into a common locus/scaffold.

^¶For organisms which express multiple actin isoforms, it has not yet been determined which isoform(s) are present in cilia/flagella.

^#The kintoun (Ktu) mutant was originally identified in medaka (Oryzias latipes) (Omran et al., 2008).

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.