Evolution of the Dynein Heavy Chain Family in Ciliates.

Dynein heavy chains are motor proteins that comprise a large gene family found across eukaryotes. We have investigated this gene family in four ciliate species: Ichthyophthirius, Oxytricha, Paramecium, and Tetrahymena. Ciliates appear to encode more dynein heavy chain genes than most eukaryotes. Phylogenetic comparisons demonstrated that the last common ancestor of the ciliates that were examined expressed at least 14 types of dynein heavy chains with most of the expansion coming from the single-headed inner arm dyneins. Each of the dyneins most likely performed different functions within the cell.

Dynein-2 and ciliogenesis in Tetrahymena.

Dynein-2 is the motor responsible for retrograde intraflagellar transport. In situ, dynein-2 comprises four subunits: the dynein-2 heavy chain (DYH2); the dynein-2 intermediate chain; the dynein-2 light-intermediate chain (D2LIC); and dynein light chain 8 (Rompolas et al. 2007. Chlamydomonas FAP133 is a dynein intermediate chain associated with the retrograde intraflagellar transport motor. J Cell Sci 120:3653-3665). In contrast to what has been reported in other model organisms, when the DYH2 gene or the D2LIC gene was disrupted in Tetrahymena, the cells continued to produce motile cilia that were not swollen or filled with material [Rajagopalan et al.2009. Dynein-2 affects the regulation of ciliary length but is not required for ciliogenesis in Tetrahymena thermophila. Mol Biol Cell 20:708-720]. When compared to wildtype cells, the dynein-2 mutants were found to have cilia that were at a lower density, shorter, and much more variable in length. One possible explanation for these effects is that the dynein-2 knockout cells grow cilia too slowly to enable them to achieve normal length and density before the cell divides. In the present study, dynein-2 knockout cells were deciliated and then allowed to regrow their cilia for 22 hr under conditions in which the cells did not divide. When dynein-2 was disabled, three effects were observed: (1) a decreased rate of cilia growth; (2) a lower cilia density that did not change over time; and (3) a wide distribution of cilia lengths that increased over time. These results confirm the importance of dynein-2 in regulating ciliary length in Tetrahymena. Cell Motil. Cytoskeleton, 2009. (c) 2009 Wiley-Liss, Inc.

Comparative genomics of the pathogenic ciliate Ichthyophthirius multifiliis, its free-living relatives and a host species provide insights into adoption of a parasitic lifestyle and prospects for disease control.

BACKGROUND: Ichthyophthirius multifiliis, commonly known as Ich, is a highly pathogenic ciliate responsible for 'white spot', a disease causing significant economic losses to the global aquaculture industry. Options for disease control are extremely limited, and Ich's obligate parasitic lifestyle makes experimental studies challenging. Unlike most well-studied protozoan parasites, Ich belongs to a phylum composed primarily of free-living members. Indeed, it is closely related to the model organism Tetrahymena thermophila. Genomic studies represent a promising strategy to reduce the impact of this disease and to understand the evolutionary transition to parasitism. RESULTS: We report the sequencing, assembly and annotation of the Ich macronuclear genome. Compared with its free-living relative T. thermophila, the Ich genome is reduced approximately two-fold in length and gene density and three-fold in gene content. We analyzed in detail several gene classes with diverse functions in behavior, cellular function and host immunogenicity, including protein kinases, membrane transporters, proteases, surface antigens and cytoskeletal components and regulators. We also mapped by orthology Ich's metabolic pathways in comparison with other ciliates and a potential host organism, the zebrafish Danio rerio. CONCLUSIONS: Knowledge of the complete protein-coding and metabolic potential of Ich opens avenues for rational testing of therapeutic drugs that target functions essential to this parasite but not to its fish hosts. Also, a catalog of surface protein-encoding genes will facilitate development of more effective vaccines. The potential to use T. thermophila as a surrogate model offers promise toward controlling 'white spot' disease and understanding the adaptation to a parasitic lifestyle.

Dynein-2 affects the regulation of ciliary length but is not required for ciliogenesis in Tetrahymena thermophila.

Eukaryotic cilia and flagella are assembled and maintained by the bidirectional intraflagellar transport (IFT). Studies in alga, nematode, and mouse have shown that the heavy chain (Dyh2) and the light intermediate chain (D2LIC) of the cytoplasmic dynein-2 complex are essential for retrograde intraflagellar transport. In these organisms, disruption of either dynein-2 component results in short cilia/flagella with bulbous tips in which excess IFT particles have accumulated. In Tetrahymena, the expression of the DYH2 and D2LIC genes increases during reciliation, consistent with their roles in IFT. However, the targeted elimination of either DYH2 or D2LIC gene resulted in only a mild phenotype. Both knockout cell lines assembled motile cilia, but the cilia were of more variable lengths and less numerous than wild-type controls. Electron microscopy revealed normally shaped cilia with no swelling and no obvious accumulations of material in the distal ciliary tip. These results demonstrate that dynein-2 contributes to the regulation of ciliary length but is not required for ciliogenesis in Tetrahymena.

Analysis of properties of cilia using Tetrahymena thermophila.

Cilia and eukaryotic flagella are important structures required for the motility of cells, the movement of medium across the surfaces of cells, and the connections between the receptor and synthetic portions of sensory cells. The axoneme forms the cytoskeleton of the cilium comprising several hundreds of proteins that assemble into the 9 + 2 arrangement of outer doublet and central pair microtubules, the inner and outer rows of dynein arms, and many other structures. Tetrahymena thermophila is an excellent model organism for the study of cilia and ciliogenesis. The cell is covered by about 1,000 cilia which are essential for survival. Additionally, the Tetrahymena genome is available and targeted genetic manipulations are straightforward. In this chapter, we describe five protocols that examine properties of cilia: (a) measuring mRNA levels to see the effect of deciliation on gene expression; (b) swimming velocity and linearity; (c) ciliary length and density; (d) phagocytosis that occurs through the ciliated oral apparatus; and (e) depolarization-induced ciliary reversal.

Identification and characterization of dynein genes in Tetrahymena.

We describe the protocol through which we identify and characterize dynein subunit genes in the ciliated protozoan Tetrahymena thermophila. The gene(s) of interest is found by searching the Tetrahymena genome, and it is characterized in silico including the prediction of the open reading frame and identification of likely introns. The gene is then characterized experimentally, including the confirmation of the exon-intron organization of the gene and the measurement of the expression of the gene in nondeciliated and reciliating cells. In order to understand the function of the gene product, the gene is modified-for example, deleted, overexpressed, or epitope-tagged-using the straightforward gene replacement strategies available with Tetrahymena. The effect(s) of the dynein gene modification is evaluated by examining transformants for ciliary traits including cell motility, ciliogenesis, cell division, and the engulfment of particles through the oral apparatus. The multistepped protocol enables undergraduate students to engage in short- and long-term experiments. In our laboratory during the last 6 years, more than two dozen undergraduate students have used these methods to investigate dynein subunit genes.

Dynein light chain family in Tetrahymena thermophila.

Dyneins are large protein complexes that produce directed movement on microtubules. In situ, dyneins comprise combinations of heavy, intermediate, light-intermediate, and light chains. The light chains regulate the locations and activities of dyneins but their functions are not completely understood. We have searched the recently sequenced Tetrahymena thermophila macronuclear genome to describe the entire family of dynein light chains expressed in this organism. We identified fourteen genes encoding putative dynein light chains and seven genes encoding light chain-like proteins. RNA-directed PCR revealed that all 21 genes were expressed. Quantitative real time reverse transcription PCR showed that many of these genes were upregulated after deciliation, indicating that these proteins are present in cilia. Using the nomenclature developed in Chlamydomonas, Tetrahymena expresses two isoforms each of LC2, LC4, LC7, and Tctex1, three isoforms of p28, and six LC8/LC8-like isoforms. Tetrahymena also expresses two LC3-like genes. No Tetrahymena orthologue was found for Chlamydomonas LC5 or LC6. This study provides a complete description of the different genes and isoforms of the dynein light chains that are expressed in Tetrahymena, a model organism in which the targeted manipulation of genes is straightforward.