Terminology and nomenclature of the cytoskeletal elements associated with the flagellar/ciliary apparatus in protists is based on Andersen, R.A., Barr, D.J.S., Lynn, D.H., Melkonian, M., Moestrup, Ø., and Sleigh, M.A. 1991. Terminology and nomenclature of the cytoskeletal elements associated with the flagellar/ciliary apparatus in protists. Protoplasma 164: 1-8. Some additions and editing changes have been made.
The terminology used to describe the cytoskeleton of protists is sometimes confusing. The independent origins of protistology from studies on algae, fungi, and protozoa contributed to these problems. The paper by Anderson and colleagues was part of an effort to achieve a common terminology so that communication would be improved. The items listed below will also be added to the overall glossary in alphabetical order.
The illustration shows color-coded regions of a cilium. The transitional region is located at the surface of the cell, and is where the 9+2 structure of the axoneme changes to the 9 X triplet structure of the basal body. Rootlets are additional cytoskeletal structures that arise in association with the basal body. The definitions that are listed below follow the sequence from top to bottom.
Cilium of Paramecium putrinum, color coded. Image by D J Patterson, copyright D J Patterson.
GENERAL TERMS
Flagellar apparatus/kinetid. An organellar complex consisting of one or more basal bodies/kinetosomes that may bear flagella/cilia, may have microtubular and fibrous roots associated with their bases, and may function in locomotion, feeding, sensation, and reproduction. There is tremendous diversity in the elements that make up the flagellar apparatus/kinetid; some elements are homologs and some are analogs. Comparisons of the flagellar apparatus/kinetid of seemingly very different taxa have suggested the existence of new monophyletic assemblages.
Flagellum/Cilium. A long, cylindrical extension of a eukaryotic cell, bounded by the plasma membrane and containing an axoneme. A flagellum/cilium is a motility organelle that is mainly involved in cell movement by means of water propulsion, but can perform additional functions such as feeding, mating, and sensory perception. The flagellum/cilium can be subdivided into different sub-compartments: (1) axoneme, (2) paraxonemal structures, (3) flagellar/ciliary matrix, (4) flagellar/ciliary membrane,and (5) flagellar/ciliary surface. In the axial direction each sub-compartment of the flagellum/cilium can often be subdivided into 3 parts: tip, shaft, and transitional region/zone. Synonyms: eukaryotic flagellum, undulipodium
Cytoskeleton. Intracellular network of protein filaments that is insoluble in non-ionic detergents. The cytoskeleton gives the cell strength, rigidity and shape, and it is responsible for cell motility and intracellular movements. The cytoskeleton of flagellate/ciliate protists consists of (1) the flagellar apparatus/kinetid, and (2) cytoskeletal protein filaments not associated with the flagellar apparatus.
Haptonema. A filamentous appendage that is (usually) relatively long, consisting of an extension of the plasma membrane, a sheath of endoplasmic reticulum, and a core of several microtubules anchored near the basal bodies/kinetosomes. Haptonemata occur on many motile prymnesiophytes (= haptophytes). Superficially, they resemble flagella/cilia when viewed with a light microscope, but their ultrastructure indicates they do not originate from axonemes. Haptonemata that are long may contract quickly to form a coil at the base of the flagella/ cilia. The functions of haptonemata include attachment and food collection.
LABELLING CONVENTIONS
Labeling of flagellum/cilium and basal body/kinetosome. Many flagellate/ciliate protists bear two flagella/cilia per cell (ciliates being an obvious exception); these two must be distinguished. This has been done with a variety of names in the individual groups: dorsal/ventral, anterior/posterior, hairy/smooth, left/right, short/long, cis/trans. The problem is to compare a specific flagellum/cilium between groups, or specifically, to establish homologies. Recent studies on flagellar/ciliary development have added a new dimension to this problem. During cell division, the flagella have a semi-conservative replication such that each daughter cell receives an existing flagellum and each forms a new one. The newly formed flagella are termed immature, and during the following cell division they transform to a more mature state. The developmental process spans at least two cell cycles before a flagellum is fully mature; it remains mature for all subsequent cell divisions. This flagellar/ciliary heterogeneity and the recognitions of flagellar transformation have led to a new means for identifying and labeling flagella/cilia and their basal bodies/kinetosomes. The oldest flagellum is Number 1, the next oldest is Number 2, etc. A uniflagellate cell may have either a Number 1 or a Number 2 flagellum, while a biflagellate cell will have both Number 1 and Number 2 flagella.
Labeling of doublets/triplets. The axonemal doublets can be labeled in some protists using either a bridge that may occur between doublets 5 and 6 or the missing dynein arm on doublet 1 (many green algae). Doublets are numbered sequentially in an anti-clockwise pattern when the flagellum is viewed from tip to base. Once the doublets are labeled, they can be followed into the cell and the triplets can be numbered accordingly.
Labeling of flagellar roots. To date, labeling of flagellar roots has been the most variable of all the cytoskeletal structures. Names have been descriptive (e.g., SRm, 4 r, Cr, 12 r in Chilomonas) or arbitrary (e.g., Rl, R2, R3, etc. in Poterioochromonas). Before the discovery of flagellar transformation, flagellar labeling was arbitrary in distantly related taxa. As a consequence, root homologies were difficult to establish. However, with consistent flagellar labeling (see above), it is possible to have consistent labeling of roots; it remains uncertain whether consistency in position and structure means homology.
Axoneme. An axial array of (usually) 9 outer doublet and 2 central microtubules. The basic architecture of the axoneme is presumably universal in eukaryotic cells and includes: outer doublet microtubules, central pair of microtubules, outer and inner dynein arms, nexin links, radial spokes, central sheath, etc. This does not mean that axonemes in different protists are identical in molecular or fine structural terms. Typically, the doublet microtubules consist of one complete microtubule with 13 subunits (A-tubule) and one partial microtubule with 10-11 subunits (B-tubule). Individual doublet microtubules can often be distinguished because variability exists in paraxonemal structures or cell surface components that enable specific doublet labeling. Some axonemal components may be modified or missing in the different protist groups. For example, the central pair of microtubules may be missing (especially in flagella/cilia that are not involved in motility), special dynein arms may be present, and septations may occur within the lumen of the B-tubules.
Excrescences. Hairs, scales and the like attached to the outer face of the membrane of the flagellum.
Flagellar scales. Organic structures of discrete size and shape, often covering the whole surface of the flagellum/cilium and generally assembled in the Golgi apparatus. Flagellar scales usually differ in structure from scales present on the cell body proper. Different scale types are usually distinguished by descriptive terms like basket scales, canistrate scales, dendritic scales, flowerpot scales, knotted scales, limulus scales, man scales, pentagonal scales, spider-web scales, square-shaped scales, tree scales.
Flagellar hairs. Filamentous appendages usually arranged in one or more rows but not covering the entire surface of a flagellum/cilium. Flagellar hairs of protists were first described in the 19th century using Loeffler's staining method for bacterial flagella. These hairy flagella were termed "Flimmergeisseln". Later, the term "mastigoneme" was introduced. Today, several very distinct types of flagellar hairs have been described. Synonyms: flimmer, mastigoneme, tinsel.
Tubular flagellar hairs. Filamentous appendages consisting of at least a hollow shaft (> 15 nm diam.) often with one or more terminal filaments. Tubular hairs are of three major types: bipartite hairs, tripartite hairs, and hair-scales. Bipartite and tripartite hairs are first assembled in the (chloroplast) endoplasmic reticulum or nuclear envelope while hair-scales are assembled in the Golgi apparatus; the former are composed principally of glycoproteins and the latter are of complex carbohydrates. Synonyms: mastigoneme.
Bipartite hairs. Filamentous appendages consisting of only a cylindrical shaft and one or more terminal filaments; characteristic of the cryptomonads. Most cryptophytes have two slightly different types of bipartite hairs: on one flagellum the hairs are relatively short and in a single row along the length of the flagellum; on the other flagellum, hairs are longer and occur in two opposite rows along the length of the flagellum. The two types of hairs may also differ in the number and length of their terminal filaments. Some cryptophytes have other arrangements of hairs. Also, the shaft bears long and short filaments in Hemiselmis but apparently lacks such filaments in the other genera. Synonyms: mastigoneme, retroneme.
Tripartite hairs. Filamentous appendages consisting of a tapered base, a cylindrical shaft and one or more terminal filaments; characteristic of many chromophyte algae, Oomycete fungi and some heterotrophic flagellates. The shaft bears long and short filaments in several groups but lacks filaments in others; hairs are usually arranged in two rows along the length of the flagellum and attached through the flagellar membrane to specific outer doublets.
Hair scales. Tubular flagellar hairs assembled in the Golgi apparatus and consisting of carbohydrates primarily, forming two rows along the longitudinal axis of the flagellum and attaching to axonemal B-tubules Numbers 4 and 8. Hair scales occur on scaly flagella of green algae.
Non-tubular flagellar hairs. Filamentous appendages less than 15 nm in diameter. Non-tubular flagellar hairs occur in various protistan groups, such as the dinoflagellates, euglenophytes, green algae (e.g., Chlamydomonas). In Chlamydomonas they consist of a single high-molecular mass glycoprotein.
Flagellar/ciliary matrix. The cytosol of the flagellum/cilium, often lacking structural detail.
Flagellar/ciliary membrane. The extension of the plasma membrane that encloses the axoneme and flagellar/ciliary matrix.
Flagellar/ciliary surface. Structures associated with the outer surface of the flagellar/ciliary membrane, including fibrillar surface coat, hairs and scales.
Flagellar wing(s). Laminar extensions of the flagellar membrane, extending along the long axis of the flagellum.
Fibrillar surface coat. Fibrous component covering the entire surface of the flagellum/cilium. Chlamydomonas and Chlamydobotrys have flagella/cilia bearing a fibrillar surface coat. Synonyms: tomentum.
Paraxonemal structures (PAS). Structures embedded in the flagellar matrix that are not part of the axoneme but often connected to specific axonemal doublets. We distinguish at least two major types, paraxonemal body and paraxonemal rod. Synonyms: paraxial structures, paraflagellar structures.
Paraxonemal body (PAB). Proteinaceous structure restricted to a certain area along the flagellum/cilium. A paraxonemal body occurs in chromophytes, euglenids and kinetoplastids; no homology is implied. Some PABs are autofluorescent, emitting green light when excited with blue light. PABs may play a role in phototactic photoreception. Some PABs are paracrystalline, linked to both the axoneme and paraxonemal fibers. "Flagellar spines" are a special type found in male gametes of oogamous brown algae. Synonyms: paraxial body, paraflagellar body (PFB), flagellar swelling.
Paraxonemal rod (PAR). Long, cylindrical structure (solid or hollow) that extends nearly the entire length of a flagellum/ cilium, located between the axoneme and flagellar membrane and usually connected to the axoneme and flagellar membrane by specific links. The paraxonemal rod occurs in dinoflagellates, euglenids, kinetoplastids, pedinellids and silicoflagellates. It may be very different in ultrastructure and biochemical composition in the different groups of protists and no homology is implied. Examples are the PAR of Euglena gracilis that is a paracrystalline, hollow structure that is non-contractile, the PAR in the transverse flagellum of dinoflagellates (= paraxonemal fiber) that is solid, cross-striated, contractile and contains the protein centrin, and the PAR of the longitudinal flagellum of dinoflagellates such as Gyrodinium that is a hollow cylinder composed of helically arranged fibrils. Synonyms: flagellar rod, paraxial rod, paraflagellar rod.
Transitional region/transitional zone. The most proximal (basal) part of a flagellum/cilium adjacent to the basal body/kinetosome; comprising matrix, axoneme, and flagellar/ciliary membrane. Comments: The transitional region is sometimes defined as the region between the proximal ends of the central pair of microtubules of the axoneme and the distal ends of the C-tubules of the basal body/kinetosome. However, we prefer a more general definition because some transitional structures cross over these boundaries. For example, the transitional helix of chromophytes and the helix of the euglenids Entosiphon extend into the region containing the central pair of microtubules of the axoneme. The transitional region may include three major components: (1) concentric fibers, (2) transitional plate, and (3) transitional fibers. It must be emphasized here that we do not imply a homology among taxa; we are only identifying positional and structural similarities. Synonyms: transition region, transition zone, flagellar transition region.
Basal apparatus. Flagellar or ciliary apparatus exclusive of flagella/cilia. Includes the basal body and associated rootlets.
Concentric fibers. Intra-axonemal structures consisting of filaments that often connect to the outer doublets of the axoneme. The filaments may be arranged as rings, a helix or a stellate structure. We distinguish at least three types of concentric fibers: (1) concentric ring fibers, (2) the transitional helix, and (3) the stellate structure. Concentric fibers are the most variable of the transitional features, and they may have evolved independently more than once.
Concentric ring fibers. A stacked series of fine concentric rings (or possibly a helix) connecting A-tubules of the axonemal doublets. This type occurs in chytrids, ciliates, euglenids, plasmodiophoromycetes, and the amoebo-flagellate Naegleria.
Transitional helix. A thick helix (or possibly stacked rings) that lies inside the outer doublets of the axoneme but apparently does not connect with them. This type occurs in many but not all chromophyte algae and Oomycete fungi. A "double helix" occurs in some Oomycetes, hyphochytriomycetes, bicosoecids, slopalinds, and the xanthophyte Heterococcus. The "coiled fiber" of the green alga Pyramimonas may belong in this category. Synonyms: coiled fiber, Spiralkorper.
Stellate structure. A cylinder consisting of a number of filaments that connect A-tubules of every second outer axonemal doublet with each other and in transverse flagellar section is seen as a star-like pattern. The stellate structure may consist of one or two parts (termed distal and proximal). If a transitional plate is intercalated between two parts of the stellate structure, the complex appears H-shaped in longitudinal flagellar section. Synonyms: star-shaped body, stellate pattern.
Transitional plate. Thin, plate-like structure oriented perpendicularly to the axoneme, usually filling the lumen of the axoneme and sometimes extending to the flagellar membrane. The transitional plate can vary significantly in its location, number and detailed structure. Synonyms: axosome, basal plate, terminal cap, terminal partition, terminal plate, transverse diaphragm, transverse septum.
Transitional fibers. Thin strands extending from a point between the A- and B-tubules to the plasma and flagellar membranes, beginning where the axoneme assumes the 9 + 2 arrangement and ending where the distal ends of the C-tubules terminate. In the flagellum/cilium, the transitional fibers are short and extend straight to the membrane. Below the transitional region they are necessarily longer and sometimes are whorled like a Catherine wheel. In chytrids the transitional fibers below the transitional region are especially large, often with secondary fibers. Synonyms: accessory spokes, anchoring fibers, curving arms, kinetosome props, links, props, struts.
Basal body /kinetosome. Cylindrical structure (ca. 0.2 µm diameter) found at the base of a flagellum/cilium (or by itself in the area of a flagellar apparatus/kinetid), consisting of a continuation of the nine outer axonemal doublets (A, B) but with the addition of a C-microtubule to form a triplet. Proximal end containing a cartwheel structure and sometimes B- and C-tubule septations. Basal bodies/kinetosomes, although often linked to flagella/cilia, may occur unattached to a flagellum. When unattached, they are termed barren, dormant or nascent, depending upon structure and state of development. Pairs of basal bodies/kinetosomes may be parallel, angled or antiparallel. The substructure of basal bodies/kinetosomes includes the cartwheel, lumen, and B-, C-tubule septations. Pairs of basal bodies/ kinetosomes are interconnected by connecting fibers.
Nascent basal body/kinetosome. Nonflagellate/nonciliate, in the process of becoming full-length; sometimes lacking B- and C-tubules. Synonyms: probasal body, prokinetosome.
Dormant basal body/kinetosome. Nonflagellate/nonciliate, fully formed with a full complement of triplet microtubules, eventually giving rise to a flagellum/cilium. These occur in many flagellate green algae (e.g., Chlamydomonas, Pedinomonas), in some euglenophytes, in some chromophytes. If the developmental status of a basal body/kinetosome that is not associated with a flagellum/cilium is unknown, it should simply be referred to as nonflagellate/nonciliate. Synonyms: non-functional basal body, non-functional kinetosome.
Barren basal body/kinetosome. Fully formed, having once given rise to a flagellum/cilium in an earlier developmental stage, but now nonflagellate/nonciliate; attached to the plasma membrane. These are found in the green alga Monomastix and the synurophyte Mallomonas spendens. If the developmental status of a basal body/kinetosome that is not associated with a flagellum/cilium is unknown, it should simply be referred to as nonflagellate/ nonciliate. Synonyms: non-functional basal body, non-functional kinetosome, vestigial basal body, vestigial kinetosome.
Parallel basal body/kinetosome. A pair of basal bodies/kinetosomes that have the same orientation.
Angled basal body/kinetosome. A pair of basal bodies/kinetosomes in which the angle subtended by the long axes of the basal bodies is greater than 0° but less than 180°, most commonly approximately orthogonal.
Antiparallel basal body/kinetosome. A pair of basal bodies/kinetosomes that have opposite polarity and whose bases are adjacent or nearly so.
Cartwheel. A hub-like central axis with radiating arm-like structures extending to the A-tubule (rarely B-tubule) of each triplet, and appearing like spokes of a wheel when the basal body/kinetosome is viewed in cross-section, located at the proximal end of a basal body/kinetosome. : Sometimes cartwheels appear to be absent; this may be an evolutionarily derived state or the result of inadequate fixation Synonyms: CW-pattern.
B- and C-tubule septations. Strands bisecting the B- and C-tubules (viewed in transverse section) of some basal bodies/kinetosomes. B-tubule septations sometimes occur along the full length of the axoneme.
Connecting fibers. Fibrillar or amorphous structure linking triplets of different basal bodies/kinetosomes with each other. A variety of adjectives have been used — amorphous, banded, dense, fan-shaped, fibrillar, filamentous, plate-like, striated. There is a bewildering array of these structures that defies classification, and at this time homologies between different protistan groups are uncertain. Centrin, a contractile protein, has been investigated at the molecular level and it occurs in the distal connecting fibers of many flagellate green algae.
Lumen. The central region of the basal body/kinetosome within the cylinder of nine triplet tubules. In the proximal part of the basal body/kinetosome the lumen is filled by the cartwheel. The lumen may appear "empty" or it may contain various inclusions such as ribosome-like particles, dense spheres, dense bodies, fibrils and amorphous clumps.
Fibrous roots. Roots composed of a bundle of filaments, the thickness of which varies in roots of different origins. Frequently, but not always, the bundles appear cross-striated. It is probable that the first types of flagellar or ciliary roots seen by light microscopy were fibrous roots. These roots have turned out to be structurally and chemically heterogenous in comparison to micro-tubular roots. In addition, cell and molecular biology studies may be necessary to determine their type by assessment of contractility, ion-binding characteristics, and ATPase activity as well as characterizing their proteins by antibody-binding tests. In some cells the fibrous roots remain superficial (near the plasma membrane) throughout their length; the ciliate "kinetodesmal fibers", the superficial "transverse striated fibre" of some dinoflagellates or the "costa" of trichomonads are of this type. In other cells the striated roots extend deep into the cell cytoplasm, like the "rhizoplast" of many flagellates or the "parabasal fibers" of many metamonads, where they may make contact with such organelles as the nucleus, Golgi apparatus, plastid or mitochondrion. Centrin, assemblin, and giardin may represent common types of proteins that are formed into fibrous roots with distinctive properties. It is clear that exciting discoveries are being made in studies on the fibrous roots of protists, but our knowledge is very elementary at present. At this time there is not enough knowledge to classify all fibrous roots in the various protists into clear-cut categories, and this must await further biochemical characterization. At present, only two different types of fibrous roots, which occur in green algae, have been characterized biochemically in detail; these are System I and System II fibers. Synonyms: rhizoplast.
Flagellar/ciliary roots. Fibrous, microtubular or amorphous structures originating at or near basal bodies/kinetosomes and terminating somewhere else in the cell but not at nearby basal bodies/kinetosomes. The two major types are fibrous roots and microtubular roots. Synonyms: flagellar rootlets.
Microtubular roots. Flagellar roots consisting of one or more microtubules originating at or near a basal body/kinetosome; the microtubules having a greater stability when compared to cytoplasmic microtubules. A-tubulin of microtubular roots is acetylated in at least some protists, and this posttranslational modification may characterize all microtubular roots. Acetylated a-tubulin stabilizes microtubules so that they fail to disassemble at low temperatures or high pressure. Microtubular roots vary in number, with one or two roots per basal body/kinetosome being common. The paths of microtubular roots are usually superficial (near the plasma membrane), and their relative directions and curvatures are of primary importance in determining the morphology of a cell. The number of microtubules per root varies from one to over 80. When more than one microtubule is present in a root, the microtubules often run parallel for considerable distances and are associated laterally via intermicrotubular linkers. Microtubular roots arise from microtubular organizing centers (MTOCs) along or near the basal bodies/kinetosomes. At this time little is known about these MTOCs. Microtubular roots change as flagella/cilia transform from immature to mature forms, but it is unknown if the MTOCs change during maturation or if there are separate MTOCs for immature and mature flagellar/ciliary roots. Some microtubular roots contain MTOCs along their surfaces, and they in turn can give rise to cytoplasmic microtubules. These cytoplasmic microtubules are usually disassembled by cold or high pressure, suggesting they are not acetylated. However, some are stable in cold or high pressure. These cytoplasmic microtubules are usually involved in a vital cell function such as maintaining morphological contours for reproduction or feeding and forming or transporting scales or scale vesicles. Synonyms: microtubular rootlets.
System I fibers. Fibrous roots made of a bundle of 2nm filaments, cross-striated with a periodicity of approximately 30 nm, largely composed of the noncontractile 34 kDa protein assemblin; usually associated with microtubular roots. System I fibers are extremely stable mechanically and biochemically and are presumed to have a stress-absorbing function in the basal apparatus. In contrast to system II fibers, they do not connect with basal body triplets. Synonyms: SMAC ( = striated microtubule associated component). Possible synonyms: costa (some), kinetodesmal fiber, parabasal fiber, striated root (some), transverse striated fiber.
System II fibers. Fibrous roots made of a bundle of 4-8 nm filaments, often cross-striated with a periodicity of > 80 nm, composed at least in part of the Ca 2 + modulated contractile protein centrin; not closely associated with root microtubules, but originating at basal body triplets. System II fibers usually extend into the cell where they often link to the nucleus, or occasionally to other organelles (plastid, mitochondrion). Some system II fibers are superficial, especially in Ulvophyceae. Synonyms: R. fiber, rhizoplast (some), striated root (some).
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