351
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Hirschner W, Pogoda HM, Kramer C, Thiess U, Hamprecht B, Wiesmüller KH, Lautner M, Verleysdonk S. Biosynthesis of Wdr16, a marker protein for kinocilia-bearing cells, starts at the time of kinocilia formation in rat, and wdr16 gene knockdown causes hydrocephalus in zebrafish. J Neurochem 2007; 101:274-88. [PMID: 17394468 DOI: 10.1111/j.1471-4159.2007.04500.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The rat ortholog of the WD40 repeat protein Wdr16 is abundantly expressed in testis and cultured ependymal cells. Low levels are found in lung and brain, respectively, while it is absent from kinocilia-free tissues. In testis and ependymal primary cultures, Wdr16 messenger RNA appears concomitantly with the messages for sperm-associated antigen 6, a kinocilia marker, and for hydin, a protein linked to ciliary function and hydrocephalus. In testis, ependyma and respiratory epithelium, the Wdr16 protein is up-regulated together with kinocilia formation. The wdr16 gene is restricted to genera in possession of kinocilia, and it is strongly conserved during evolution. The human and zebrafish proteins are identical in 62% of their aligned amino acids. On the message level, the zebrafish Wdr16 ortholog was found exclusively in kinocilia-bearing tissues by in situ hybridisation. Gene knockdown in zebrafish embryos by antisense morpholino injection resulted in severe hydrocephalus formation with unaltered ependymal morphology or ciliary beat. Wdr16 can be considered a differentiation marker of kinocilia-bearing cells. In the brain, it appears to be functionally related to water homeostasis or osmoregulation.
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Affiliation(s)
- Wolfgang Hirschner
- Interfaculty Institute for Biochemistry, University of Tuebingen, Tuebingen, Germany
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352
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Abd El-Aziz MM, Barragan I, O'Driscoll C, Borrego S, Abu-Safieh L, Pieras JI, El-Ashry MF, Prigmore E, Carter N, Antinolo G, Bhattacharya SS. Large-scale molecular analysis of a 34 Mb interval on chromosome 6q: major refinement of the RP25 interval. Ann Hum Genet 2007; 72:463-77. [PMID: 18510646 PMCID: PMC2689154 DOI: 10.1111/j.1469-1809.2008.00455.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
A large scale bioinformatics and molecular analysis of a 34 Mb interval on chromosome 6q12 was undertaken as part of our ongoing study to identify the gene responsible for an autosomal recessive retinitis pigmentosa (arRP) locus, RP25. Extensive bioinformatics analysis indicated in excess of 110 genes within the region and we also noted unfinished sequence on chromosome 6q in the Human Genome Database, between 58 and 61.2 Mb. Forty three genes within the RP25 interval were considered as good candidates for mutation screening. Direct sequence analysis of the selected genes in 7 Spanish families with arRP revealed a total of 244 sequence variants, of which 67 were novel but none were pathogenic. This, together with previous reports, excludes 60 genes within the interval ( approximately 55%) as disease causing for RP. To investigate if copy number variation (CNV) exists within RP25, a comparative genomic hybridization (CGH) analysis was performed on a consanguineous family. A clone from the tiling path array, chr6tp-19C7, spanning approximately 100-Kb was found to be deleted in all affected members of the family, leading to a major refinement of the interval. This will eventually have a significant impact on cloning of the RP25 gene.
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Affiliation(s)
- M M Abd El-Aziz
- Department of Molecular Genetics, Institute of Ophthalmology, London EC1V 9EL, UK. Department of Ophthalmology, Tanta University Hospital, Tanta, Egypt
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353
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Griffiths S, Portman N, Taylor PR, Gordon S, Ginger ML, Gull K. RNA interference mutant induction in vivo demonstrates the essential nature of trypanosome flagellar function during mammalian infection. EUKARYOTIC CELL 2007; 6:1248-50. [PMID: 17513568 PMCID: PMC1951115 DOI: 10.1128/ec.00110-07] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We demonstrate that trypanosomes compromised in flagellar function are rapidly cleared from infected mice. Analysis of the PFR2 bloodstream RNA interference mutant revealed that defective cell motility occurred prior to cytokinesis failure. This validation provides a paradigm for the flagellum as a target for future assays and interventions against this human pathogen.
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Affiliation(s)
- Samantha Griffiths
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, United Kingdom
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354
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Liu Q, Tan G, Levenkova N, Li T, Pugh EN, Rux JJ, Speicher DW, Pierce EA. The proteome of the mouse photoreceptor sensory cilium complex. Mol Cell Proteomics 2007; 6:1299-317. [PMID: 17494944 PMCID: PMC2128741 DOI: 10.1074/mcp.m700054-mcp200] [Citation(s) in RCA: 289] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Primary cilia play critical roles in many aspects of biology. Specialized versions of primary cilia are involved in many aspects of sensation. The single photoreceptor sensory cilium (PSC) or outer segment elaborated by each rod and cone photoreceptor cell of the retina is a classic example. Mutations in genes that encode cilia components are common causes of disease, including retinal degenerations. The protein components of mammalian primary and sensory cilia have not been defined previously. Here we report a detailed proteomics analysis of the mouse PSC complex. The PSC complex comprises the outer segment and its cytoskeleton, including the axoneme, basal body, and ciliary rootlet, which extends into the inner segment of photoreceptor cells. The PSC complex proteome contains 1968 proteins represented by three or more unique peptides, including approximately 1500 proteins not detected in cilia from lower organisms. This includes 105 hypothetical proteins and 60 proteins encoded by genes that map within the critical intervals for 23 inherited cilia-related disorders, increasing their priority as candidate genes. The PSC complex proteome also contains many cilia proteins not identified previously in photoreceptors, including 13 proteins produced by genes that harbor mutations that cause cilia disease and seven intraflagellar transport proteins. Analyses of PSC complexes from rootletin knock-out mice, which lack ciliary rootlets, confirmed that 1185 of the identified PSC complex proteins are derived from the outer segment. The mass spectrometry data, benchmarked by 15 well characterized outer segment proteins, were used to quantify the copy number of each protein in a mouse rod outer segment. These results reveal mammalian cilia to be several times more complex than the cilia of unicellular organisms and open novel avenues for studies of how cilia are built and maintained and how these processes are disrupted in human disease.
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Affiliation(s)
- Qin Liu
- F. M. Kirby Center for Molecular Ophthalmology, Scheie Eye Institute, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
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355
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Ou G, Koga M, Blacque OE, Murayama T, Ohshima Y, Schafer JC, Li C, Yoder BK, Leroux MR, Scholey JM. Sensory ciliogenesis in Caenorhabditis elegans: assignment of IFT components into distinct modules based on transport and phenotypic profiles. Mol Biol Cell 2007; 18:1554-69. [PMID: 17314406 PMCID: PMC1855012 DOI: 10.1091/mbc.e06-09-0805] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2006] [Revised: 02/02/2007] [Accepted: 02/07/2007] [Indexed: 01/06/2023] Open
Abstract
Sensory cilium biogenesis within Caenorhabditis elegans neurons depends on the kinesin-2-dependent intraflagellar transport (IFT) of ciliary precursors associated with IFT particles to the axoneme tip. Here we analyzed the molecular organization of the IFT machinery by comparing the in vivo transport and phenotypic profiles of multiple proteins involved in IFT and ciliogenesis. Based on their motility in wild-type and bbs (Bardet-Biedl syndrome) mutants, IFT proteins were classified into groups with similar transport profiles that we refer to as "modules." We also analyzed the distribution and transport of fluorescent IFT particles in multiple known ciliary mutants and 49 new ciliary mutants. Most of the latter mutants were snip-SNP mapped and one, namely dyf-14(ks69), was cloned and found to encode a conserved protein essential for ciliogenesis. The products of these ciliogenesis genes could also be assigned to the aforementioned set of modules or to specific aspects of ciliogenesis, based on IFT particle dynamics and ciliary mutant phenotypes. Although binding assays would be required to confirm direct physical interactions, the results are consistent with the hypothesis that the C. elegans IFT machinery has a modular design, consisting of modules IFT-subcomplex A, IFT-subcomplex B, and a BBS protein complex, in addition to motor and cargo modules, with each module contributing to distinct functional aspects of IFT or ciliogenesis.
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Affiliation(s)
- Guangshuo Ou
- *Center for Genetics and Development, Section of Molecular and Cellular Biology, University of California, Davis, CA 95616
| | - Makato Koga
- Department of Biology, Faculty of Sciences, Kyushu University Graduate School, 6-10-1, Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan
| | - Oliver E. Blacque
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
- School of Biomolecular and Biomedical Science, University College Dublin Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland; and
| | - Takashi Murayama
- Department of Biology, Faculty of Sciences, Kyushu University Graduate School, 6-10-1, Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan
| | - Yasumi Ohshima
- Department of Biology, Faculty of Sciences, Kyushu University Graduate School, 6-10-1, Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan
| | - Jenny C. Schafer
- Department of Cell Biology, University of Alabama at Birmingham Medical Center, Birmingham, AL 35294
| | - Chunmei Li
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Bradley K. Yoder
- Department of Cell Biology, University of Alabama at Birmingham Medical Center, Birmingham, AL 35294
| | - Michel R. Leroux
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Jonathan M. Scholey
- *Center for Genetics and Development, Section of Molecular and Cellular Biology, University of California, Davis, CA 95616
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356
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Dawe HR, Farr H, Gull K. Centriole/basal body morphogenesis and migration during ciliogenesis in animal cells. J Cell Sci 2007; 120:7-15. [PMID: 17182899 DOI: 10.1242/jcs.03305] [Citation(s) in RCA: 194] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Cilia, either motile or immotile, exist on most cells in the human body. There are several different mechanisms of ciliogenesis, which enable the production of many kinds of cilia and flagella: motile and immotile, transient and long-lived. These can be linked to the cell cycle or associated with differentiation. A primary cilium is extended from a basal body analogous to the mitotic centrioles, whereas the several hundred centrioles needed to form the cilia of a multi-ciliated cell can be generated by centriolar or acentriolar pathways. Little is known about the molecular control of these pathways and most of our knowledge comes from ultrastructural studies. The increasing number of genetic diseases linked to dysfunctional cilia and basal bodies has renewed interest in this area, and recent proteomic and cell biological studies in model organisms have helped to shed light on the molecular components of these enigmatic organelles.
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Affiliation(s)
- Helen R Dawe
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK.
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357
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Baron DM, Kabututu ZP, Hill KL. Stuck in reverse: loss of LC1 in Trypanosoma brucei disrupts outer dynein arms and leads to reverse flagellar beat and backward movement. J Cell Sci 2007; 120:1513-20. [PMID: 17405810 DOI: 10.1242/jcs.004846] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Axonemal dyneins are multisubunit molecular motors that provide the driving force for flagellar motility. Dynein light chain 1 (LC1) has been well studied in Chlamydomonas reinhardtii and is unique among all dynein components as the only protein known to bind directly to the catalytic motor domain of the dynein heavy chain. However, the role of LC1 in dynein assembly and/or function is unknown because no mutants have previously been available. We identified an LC1 homologue (TbLC1) in Trypanosoma brucei and have investigated its role in trypanosome flagellar motility using epitope tagging and RNAi studies. TbLC1 is localized along the length of the flagellum and partitions between the axoneme and soluble fractions following detergent and salt extraction. RNAi silencing of TbLC1 gene expression results in the complete loss of the dominant tip-to-base beat that is a hallmark of trypanosome flagellar motility and the concomitant emergence of a sustained reverse beat that propagates base-to-tip and drives cell movement in reverse. Ultrastructure analysis revealed that outer arm dyneins are disrupted in TbLC1 mutants. Therefore LC1 is required for stable dynein assembly and forward motility in T. brucei. Our work provides the first functional analysis of LC1 in any organism. Together with the recent findings in T. brucei DNAI1 mutants [Branche et al. (2006). Conserved and specific functions of axoneme components in trypanosome motility. J. Cell Sci. 119, 3443-3455], our data indicate functionally specialized roles for outer arm dyneins in T. brucei and C. reinhardtii. Understanding these differences will provide a more robust description of the fundamental mechanisms underlying flagellar motility and will aid efforts to exploit the trypanosome flagellum as a drug target.
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Affiliation(s)
- Desiree M Baron
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA 90095, USA
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358
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Lefièvre L, Bedu-Addo K, Conner SJ, Machado-Oliveira GSM, Chen Y, Kirkman-Brown JC, Afnan MA, Publicover SJ, Ford WCL, Barratt CLR. Counting sperm does not add up any more: time for a new equation? Reproduction 2007; 133:675-84. [PMID: 17504912 DOI: 10.1530/rep-06-0332] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Although sperm dysfunction is the single most common cause of infertility, we have poor methods of diagnosis and surprisingly no effective treatment (excluding assisted reproductive technology). In this review, we challenge the usefulness of a basic semen analysis and argue that a new paradigm is required immediately. We discuss the use of at-home screening to potentially improve the diagnosis of the male and to streamline the management of the sub-fertile couple. Additionally, we outline the recent progress in the field, for example, in proteomics, which will allow the development of new biomarkers of sperm function. This new knowledge will transform our understanding of the spermatozoon as a machine and is likely to lead to non-ART treatments for men with sperm dysfunction.
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Affiliation(s)
- Linda Lefièvre
- Reproductive Biology and Genetics Group, Division of Reproductive and Child Health, The Medical School, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
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359
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Kelly S, Reed J, Kramer S, Ellis L, Webb H, Sunter J, Salje J, Marinsek N, Gull K, Wickstead B, Carrington M. Functional genomics in Trypanosoma brucei: a collection of vectors for the expression of tagged proteins from endogenous and ectopic gene loci. Mol Biochem Parasitol 2007; 154:103-9. [PMID: 17512617 PMCID: PMC2705915 DOI: 10.1016/j.molbiopara.2007.03.012] [Citation(s) in RCA: 157] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2007] [Revised: 03/20/2007] [Accepted: 03/21/2007] [Indexed: 11/23/2022]
Affiliation(s)
- Steven Kelly
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Jenny Reed
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Susanne Kramer
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Louise Ellis
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Helena Webb
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Jack Sunter
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Jeanne Salje
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Nina Marinsek
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Keith Gull
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Bill Wickstead
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Mark Carrington
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
- Corresponding author. Tel.: +44 1223 333683; fax: +44 1223 766002.
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360
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Inaba K. Molecular basis of sperm flagellar axonemes: structural and evolutionary aspects. Ann N Y Acad Sci 2007; 1101:506-26. [PMID: 17363437 DOI: 10.1196/annals.1389.017] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The axonemes serve as motile machineries in sperm flagella. Although atypical axonemal structures are observed in some cases, 9 + 2 microtubule structure of the axoneme is predominant in many organisms. Several structures are bound to these microtubules and comprise a highly organized protein network. Extensive proteomic analysis of the axonemes has led to find several repeats, domains, and motifs in axonemal proteins. Molecular comparison of subunit composition of axonemal substructures between the ascidian Ciona intestinalis and the green algae Chlamydomonas reinhardtti leads to an intriguing molecular aspect concerning the evolution of intracellular functional complex: The architecture of the axonemes has been well conserved through evolution, but the molecular structure of each axonemal component is not always conserved. In light of domain structure in the axonemal proteins, substructures like outer arm dynein and radial spoke contain a set of domain structures, although some domain-containing subunits are different between these two organisms. Thus, conservation of protein domains within a substructure seems to take precedence over that of each protein ("module-dominant conservation"), which may ultimately result in morphological and functional conservation of the axonemes through evolution.
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Affiliation(s)
- Kazuo Inaba
- Shimoda Marine Research Center, University of Tsukuba, 5-10-1 Shimoda, Shizuoka 415-0025, Japan.
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361
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Lechtreck KF, Witman GB. Chlamydomonas reinhardtii hydin is a central pair protein required for flagellar motility. J Cell Biol 2007; 176:473-82. [PMID: 17296796 PMCID: PMC2063982 DOI: 10.1083/jcb.200611115] [Citation(s) in RCA: 135] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2006] [Accepted: 01/06/2007] [Indexed: 11/22/2022] Open
Abstract
Mutations in Hydin cause hydrocephalus in mice, and HYDIN is a strong candidate for causing hydrocephalus in humans. The gene is conserved in ciliated species, including Chlamydomonas reinhardtii. An antibody raised against C. reinhardtii hydin was specific for an approximately 540-kD flagellar protein that is missing from axonemes of strains that lack the central pair (CP). The antibody specifically decorated the C2 microtubule of the CP apparatus. An 80% knock down of hydin resulted in short flagella lacking the C2b projection of the C2 microtubule; the flagella were arrested at the switch points between the effective and recovery strokes. Biochemical analyses revealed that hydin interacts with the CP proteins CPC1 and kinesin-like protein 1 (KLP1). In conclusion, C. reinhardtii hydin is a CP protein required for flagellar motility and probably involved in the CP-radial spoke control pathway that regulates dynein arm activity. Hydrocephalus caused by mutations in hydin likely involves the malfunctioning of cilia because of a defect in the CP.
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Affiliation(s)
- Karl-Ferdinand Lechtreck
- Department of Cell Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA.
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362
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Smith EF. Hydin seek: finding a function in ciliary motility. J Cell Biol 2007; 176:403-4. [PMID: 17296793 PMCID: PMC2063975 DOI: 10.1083/jcb.200701113] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2007] [Accepted: 01/23/2007] [Indexed: 11/22/2022] Open
Abstract
One of the most surprising discoveries in cell biology in the past 5-10 years is the number of diverse human diseases that result from defects in ciliary assembly and/or motility, so-called ciliopathies (Badano, J.L., N. Mitsuma, P.L. Beales, and N. Katsanis. 2006. Annu. Rev. Genomics Hum. Genet. 7:125-148). The results presented by Lechtreck and Witman (see p. 473 of this issue) provide yet another example of how work in the model organism Chlamydomonas reinhardtii can reveal important insights into the underlying mechanisms of ciliary assembly/function and the diseases associated with defects in these organelles. By taking advantage of the wide array of experimental approaches C. reinhardtii offers, Lechtreck and Witman determined the precise axonemal location of hydin, a protein that, when mutated, causes hydrocephalus, and defined a unique role for hydin in ciliary motility.
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Affiliation(s)
- Elizabeth F Smith
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA.
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363
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Hammarton TC. Cell cycle regulation in Trypanosoma brucei. Mol Biochem Parasitol 2007; 153:1-8. [PMID: 17335918 PMCID: PMC1914216 DOI: 10.1016/j.molbiopara.2007.01.017] [Citation(s) in RCA: 120] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2006] [Revised: 01/25/2007] [Accepted: 01/26/2007] [Indexed: 01/23/2023]
Abstract
Cell division is regulated by intricate and interconnected signal transduction pathways that precisely coordinate, in time and space, the complex series of events involved in replicating and segregating the component parts of the cell. In Trypanosoma brucei, considerable progress has been made over recent years in identifying molecular regulators of the cell cycle and elucidating their functions, although many regulators undoubtedly remain to be identified, and there is still a long way to go with respect to determining signal transduction pathways. However, it is clear that cell cycle regulation in T. brucei is unusual in many respects. Analyses of trypanosome orthologues of conserved eukaryotic cell cycle regulators have demonstrated divergence of their function in the parasite, and a number of other key regulators are missing from T. brucei. Cell cycle regulation differs in different parasite life cycle stages, and T. brucei appears to use different checkpoint control strategies compared to model eukaryotes. It is therefore probable that T. brucei has evolved novel pathways to control its cell cycle.
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Affiliation(s)
- Tansy C Hammarton
- Division of Infection & Immunity and Wellcome Centre for Molecular Parasitology, University of Glasgow, Biomedical Research Centre, 120 University Place, Glasgow G12 8TA, United Kingdom.
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364
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Siepen JA, Swainston N, Jones AR, Hart SR, Hermjakob H, Jones P, Hubbard SJ. An informatic pipeline for the data capture and submission of quantitative proteomic data using iTRAQ. Proteome Sci 2007; 5:4. [PMID: 17270041 PMCID: PMC1796855 DOI: 10.1186/1477-5956-5-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2006] [Accepted: 02/01/2007] [Indexed: 01/25/2023] Open
Abstract
Background Proteomics continues to play a critical role in post-genomic science as continued advances in mass spectrometry and analytical chemistry support the separation and identification of increasing numbers of peptides and proteins from their characteristic mass spectra. In order to facilitate the sharing of this data, various standard formats have been, and continue to be, developed. Still not fully mature however, these are not yet able to cope with the increasing number of quantitative proteomic technologies that are being developed. Results We propose an extension to the PRIDE and mzData XML schema to accommodate the concept of multiple samples per experiment, and in addition, capture the intensities of the iTRAQTM reporter ions in the entry. A simple Java-client has been developed to capture and convert the raw data from common spectral file formats, which also uses a third-party open source tool for the generation of iTRAQTM reported intensities from Mascot output, into a valid PRIDE XML entry. Conclusion We describe an extension to the PRIDE and mzData schemas to enable the capture of quantitative data. Currently this is limited to iTRAQTM data but is readily extensible for other quantitative proteomic technologies. Furthermore, a software tool has been developed which enables conversion from various mass spectrum file formats and corresponding Mascot peptide identifications to PRIDE formatted XML. The tool represents a simple approach to preparing quantitative and qualitative data for submission to repositories such as PRIDE, which is necessary to facilitate data deposition and sharing in public domain database. The software is freely available from .
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Affiliation(s)
| | - Neil Swainston
- Manchester Interdisciplinary Biocentre, University of Manchester, UK
| | - Andrew R Jones
- Faculty of Life Sciences, University of Manchester, M13 9PT, UK
- School of Computer Science, Faculty of Engineering and Physical Sciences, University of Manchester, UK
| | - Sarah R Hart
- MBCMS, School of Chemistry, Manchester Interdisciplinary Biocentre, University of Manchester, UK
| | - Henning Hermjakob
- EMBL Outstation EBI, Wellcome Trust Genome Campus, Hinxton, Cambs, UK
| | - Philip Jones
- EMBL Outstation EBI, Wellcome Trust Genome Campus, Hinxton, Cambs, UK
| | - Simon J Hubbard
- Faculty of Life Sciences, University of Manchester, M13 9PT, UK
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365
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Li SQ, Fung MC, Reid SA, Inoue N, Lun ZR. Immunization with recombinant beta-tubulin fromTrypanosoma evansiinduced protection againstT. evansi,T. equiperdumandT. b. bruceiinfection in mice. Parasite Immunol 2007; 29:191-9. [PMID: 17371456 DOI: 10.1111/j.1365-3024.2006.00933.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The beta-tubulin gene of Trypanosoma evansi (STIB 806) was cloned and expressed in Escherichia coli. The predicted amino acid sequence of T. evansi beta-tubulin shows 100%, 99.8%, 99.1%, and 98.6% homology with T. equiperdum, T. b. brucei, T. cruzi and T. danilewskyi, respectively, but is diverse from that of T. cyclops, showing only 51.6% of homology. Recombinant beta-tubulin was expressed as inclusion bodies in E. coli. It was purified and renatured for immunological studies. Mice immunized with the renatured recombinant beta-tubulin were protected from lethal challenge with T. evansi STIB 806, T. equiperdum STIB 818 and T. b. brucei STIB 940, showing 83.3%, 70% and 76.7% protection, respectively. Serum collected from the rabbit immunized with recombinant beta-tubulin inhibited the growth of T. evansi, T. equiperdum and T. b. brucei in vitro. Serum from mice and rabbits immunized with recombinant beta-tubulin recognized only T. evansi beta-tubulin and not mouse beta-tubulin. The results of this study demonstrated that the recombinant T. evansi beta-tubulin is a potential candidate for the development of a vaccine to prevent animal trypanosomiasis caused by these three trypanosome species.
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Affiliation(s)
- S-Q Li
- Centre for Parasitic Organisms, State Key Laboratory of Biocontrol and Key Laboratory for Tropical Diseases Control of the Ministry of Education, School of Life Sciences, Sun Yat-Sen (Zhongshan) University, Guangzhou, P.R. China
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366
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Baron DM, Ralston KS, Kabututu ZP, Hill KL. Functional genomics in Trypanosoma brucei identifies evolutionarily conserved components of motile flagella. J Cell Sci 2007; 120:478-91. [PMID: 17227795 DOI: 10.1242/jcs.03352] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Cilia and flagella are highly conserved, complex organelles involved in a variety of important functions. Flagella are required for motility of several human pathogens and ciliary defects lead to a variety of fatal and debilitating human diseases. Many of the major structural components of cilia and flagella are known, but little is known about regulation of flagellar beat. Trypanosoma brucei, the causative agent of African sleeping sickness, provides an excellent model for studying flagellar motility. We have used comparative genomics to identify a core group of 50 genes unique to organisms with motile flagella. These genes, referred to as T. brucei components of motile flagella (TbCMF) include 30 novel genes, and human homologues of many of the TbCMF genes map to loci associated with human ciliary diseases. To characterize TbCMF protein function we used RNA interference to target 41 TbCMF genes. Sedimentation assays and direct observation demonstrated clear motility defects in a majority of these knockdown mutants. Epitope tagging, fluorescence localization and biochemical fractionation demonstrated flagellar localization for several TbCMF proteins. Finally, ultrastructural analysis identified a family of novel TbCMF proteins that function to maintain connections between outer doublet microtubules, suggesting that they are the first identified components of nexin links. Overall, our results provide insights into the workings of the eukaryotic flagellum, identify several novel human disease gene candidates, reveal unique aspects of the trypanosome flagellum and underscore the value of T. brucei as an experimental system for studying flagellar biology.
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Affiliation(s)
- Desiree M Baron
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA 90095, USA
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367
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Abstract
The accurate duplication of cellular organelles is important to ensure propagation through successive generations. The semi-conserved replication of DNA and DNA-containing organelles has been well studied, but the mechanisms used to duplicate most other organelles remain elusive. These include the centrosomes, which act as microtubule organizing centres during interphase and orient the mitotic spindle poles during mitosis. Centrosomes can also act as basal bodies, nucleating the growth of cilia or flagella. Even less understood are the mechanisms used to duplicate membrane-bound organelles that do not contain DNA. These include organelles involved in the secretory pathway such as the endoplasmic reticulum and the Golgi apparatus. This review will summarize the current knowledge of Golgi biogenesis in simple eukaryotic organisms, in particular, two protozoan parasites, Toxoplasma gondii and Trypanosoma brucei.
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Affiliation(s)
- Cynthia Y He
- Department of Cell Biology, Ludwig Institute for Cancer Research, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520-8002, USA.
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368
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Ralston KS, Hill KL. Trypanin, a component of the flagellar Dynein regulatory complex, is essential in bloodstream form African trypanosomes. PLoS Pathog 2006; 2:e101. [PMID: 17009870 PMCID: PMC1579245 DOI: 10.1371/journal.ppat.0020101] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2006] [Accepted: 08/23/2006] [Indexed: 11/18/2022] Open
Abstract
The Trypanosoma brucei flagellum is a multifunctional organelle with critical roles in motility, cellular morphogenesis, and cell division. Although motility is thought to be important throughout the trypanosome lifecycle, most studies of flagellum structure and function have been restricted to the procyclic lifecycle stage, and our knowledge of the bloodstream form flagellum is limited. We have previously shown that trypanin functions as part of a flagellar dynein regulatory system that transmits regulatory signals from the central pair apparatus and radial spokes to axonemal dyneins. Here we investigate the requirement for this dynein regulatory system in bloodstream form trypanosomes. We demonstrate that trypanin is localized to the flagellum of bloodstream form trypanosomes, in a pattern identical to that seen in procyclic cells. Surprisingly, trypanin RNA interference is lethal in the bloodstream form. These knockdown mutants fail to initiate cytokinesis, but undergo multiple rounds of organelle replication, accumulating multiple flagella, nuclei, kinetoplasts, mitochondria, and flagellum attachment zone structures. These findings suggest that normal flagellar beat is essential in bloodstream form trypanosomes and underscore the emerging concept that there is a dichotomy between trypanosome lifecycle stages with respect to factors that contribute to cell division and cell morphogenesis. This is the first time that a defined dynein regulatory complex has been shown to be essential in any organism and implicates the dynein regulatory complex and other enzymatic regulators of flagellar motility as candidate drug targets for the treatment of African sleeping sickness. African trypanosomes are protozoan parasites that cause African sleeping sickness, a fatal disease with devastating health and economic consequences. These parasites are indigenous to a 9 million-km2 area of sub-Saharan Africa where 60 million people live at risk of infection every day. In addition to the tremendous human health burden posed by trypanosomes, their infection of wild and domestic animals presents a barrier to sustained economic development of vast regions of otherwise productive land. Current drugs used for treatment of sleeping sickness are antiquated, toxic, and often ineffective; thus, there is a dire need for the development of innovative approaches for therapeutic intervention. Trypanosomes are highly motile and this motility requires coordinated regulation of axonemal dynein, a molecular motor that drives beating of the parasite's flagellum. In the present work, the authors demonstrate that the protein trypanin, which is part of a signaling system that regulates the flagellar dynein motor, is essential in bloodstream stage African trypanosomes. This surprising finding raises the possibility that numerous enzymes and regulatory proteins that are necessary for flagellar motility may represent novel targets for chemotherapeutic intervention in African sleeping sickness.
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Affiliation(s)
- Katherine S Ralston
- Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, California, United States of America
| | - Kent L Hill
- Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, California, United States of America
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, California, United States of America
- * To whom correspondence should be addressed. E-mail:
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369
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Oberholzer M, Bregy P, Marti G, Minca M, Peier M, Seebeck T. Trypanosomes and mammalian sperm: one of a kind? Trends Parasitol 2006; 23:71-7. [PMID: 17174157 DOI: 10.1016/j.pt.2006.12.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2006] [Revised: 11/02/2006] [Accepted: 12/06/2006] [Indexed: 01/20/2023]
Abstract
Flagellar-mediated motility is an indispensable function for cell types as evolutionarily distant as mammalian sperm and kinetoplastid parasites, a large group of flagellated protozoa that includes several important human pathogens. Despite the obvious importance of flagellar motility, little is known about the signalling processes that direct the frequency and wave shape of the flagellar beat, or those that provide the motile cell with the necessary environmental cues that enable it to aim its movement. Similarly, the energetics of the flagellar beat and the problem of a sufficient ATP supply along the entire length of the beating flagellum remain to be explored. Recent proteome projects studying the flagella of mammalian sperm and kinetoplastid parasites have provided important information and have indicated a surprising degree of similarities between the flagella of these two cell types.
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Affiliation(s)
- Michael Oberholzer
- Institute of Cell Biology, University of Bern, CH-3012 Bern, Switzerland
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370
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Oberholzer M, Marti G, Baresic M, Kunz S, Hemphill A, Seebeck T. The Trypanosoma brucei cAMP phosphodiesterases TbrPDEB1 and TbrPDEB2: flagellar enzymes that are essential for parasite virulence. FASEB J 2006; 21:720-31. [PMID: 17167070 DOI: 10.1096/fj.06-6818com] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Cyclic nucleotide specific phosphodiesterases (PDEs) are pivotal regulators of cellular signaling. They are also important drug targets. Besides catalytic activity and substrate specificity, their subcellular localization and interaction with other cell components are also functionally important. In contrast to the mammalian PDEs, the significance of PDEs in protozoal pathogens remains mostly unknown. The genome of Trypanosoma brucei, the causative agent of human sleeping sickness, codes for five different PDEs. Two of these, TbrPDEB1 and TbrPDEB2, are closely similar, cAMP-specific PDEs containing two GAF-domains in their N-terminal regions. Despite their similarity, these two PDEs exhibit different subcellular localizations. TbrPDEB1 is located in the flagellum, whereas TbrPDEB2 is distributed between flagellum and cytoplasm. RNAi against the two mRNAs revealed that the two enzymes can complement each other but that a simultaneous ablation of both leads to cell death in bloodstream form trypanosomes. RNAi against TbrPDEB1 and TbrPDEB2 also functions in vivo where it completely prevents infection and eliminates ongoing infections. Our data demonstrate that TbrPDEB1 and TbrPDEB2 are essential for virulence, making them valuable potential targets for new PDE-inhibitor based trypanocidal drugs. Furthermore, they are compatible with the notion that the flagellum of T. brucei is an important site of cAMP signaling.
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371
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Gherman A, Davis EE, Katsanis N. The ciliary proteome database: an integrated community resource for the genetic and functional dissection of cilia. Nat Genet 2006; 38:961-2. [PMID: 16940995 DOI: 10.1038/ng0906-961] [Citation(s) in RCA: 236] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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372
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Andersen JS, Mann M. Organellar proteomics: turning inventories into insights. EMBO Rep 2006; 7:874-9. [PMID: 16953200 PMCID: PMC1559674 DOI: 10.1038/sj.embor.7400780] [Citation(s) in RCA: 142] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2006] [Accepted: 07/07/2006] [Indexed: 11/08/2022] Open
Abstract
Subcellular organization is yielding to large-scale analysis. Researchers are now applying robust mass-spectrometry-based proteomics methods to obtain an inventory of biochemically isolated organelles that contain hundreds of proteins. High-resolution methods allow accurate protein identification, and novel algorithms can distinguish genuine from co-purifying components. Organellar proteomes have been analysed by bioinformatic methods and integrated with other large-scale data sets. The dynamics of organelles can also be studied by quantitative proteomics, which offers powerful methods that are complementary to fluorescence-based microscopy. Here, we review the emerging trends in this rapidly expanding area and discuss the role of organellar proteomics in the context of functional genomics and systems biology.
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Affiliation(s)
- Jens S Andersen
- Centre for Experimental Bioinformatics (CEBI), University of Southern Denmark, Campusvej 55, DK-5230 Odense, Denmark
Tel: +45 6550 2365; Fax: +45 6593 3018
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max-Planck Institute for Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
Tel: +49 89 8578 2557; Fax: +49 89 8578 2219;
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373
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Abstract
Cilia are microtubule-based organelles that project like antennae from the surface of most cells in the body. Motile cilia move fluid past cells, for example mucus in the airway. Non-motile primary cilia, however, transduce a multitude of sensory stimuli, including chemical concentrations of growth factors, hormones, odorants, and developmental morphogens, as well as osmolarity, light intensity, and fluid flow. Cilia have evolved a complex ultrastructure to accommodate these diverse functions, and an extensive molecular machinery has developed to support the assembly of these organelles. Defects in the cilia themselves, or the machinery required to assemble them, lead to a broad spectrum of human disease symptoms, including polycystic kidney disease, nephronophthisis, hydrocephalus, polydactyly, situs inversus, retinal degeneration, and obesity. While these diseases highlight the pivotal roles of cilia in physiology and development, the mechanistic link between cilia, physiology, and disease remains unclear.
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Affiliation(s)
- Wallace F Marshall
- Department of Biochemistry and Biophysics, University of California San Francisco, 600 16th St., San Francisco, California 94143, USA.
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374
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Davidge JA, Chambers E, Dickinson HA, Towers K, Ginger ML, McKean PG, Gull K. Trypanosome IFT mutants provide insight into the motor location for mobility of the flagella connector and flagellar membrane formation. J Cell Sci 2006; 119:3935-43. [PMID: 16954145 DOI: 10.1242/jcs.03203] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The flagella connector (FC) of procyclic trypanosomes is a mobile, transmembrane junction important in providing cytotactic morphogenetic information to the daughter cell. Quantitative analyses of FC positioning along the old flagellum, involving direct observations and use of the MPM2 anti-phosphoprotein monoclonal reveals a `stop point' is reached on the old flagellum which correlates well with the initiation of basal body migration and kinetoplast segregation. This demonstrates further complexities of the FC and its movement in morphogenetic events in trypanosomes than have hitherto been described. We used intraflagellar transport RNAi mutants to ablate the formation of a new flagellum. Intriguingly the FC could still move, indicating that a motor function beyond the new flagellum is sufficient to move it. When such a FC moves, it drags a sleeve of new flagellar membrane out of the flagellar pocket. This axoneme-less flagellar membrane maintains appropriate developmental relationships to the cell body including following the correct helical path and being connected to the internal cytoskeleton by macula adherens junctions. Movement of the FC in the apparent absence of intraflagellar transport raises the possibility of a new form of motility within a eukaryotic flagellum.
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Affiliation(s)
- Jacqueline A Davidge
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
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375
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Davis EE, Brueckner M, Katsanis N. The emerging complexity of the vertebrate cilium: new functional roles for an ancient organelle. Dev Cell 2006; 11:9-19. [PMID: 16824949 DOI: 10.1016/j.devcel.2006.06.009] [Citation(s) in RCA: 112] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Cilia and flagella are found on the surface of a strikingly diverse range of cell types. These intriguing organelles, with their unique and highly adapted protein transport machinery, have been studied extensively in the context of cellular locomotion, sexual reproduction, or fluid propulsion. However, recent studies are beginning to show that in vertebrates particularly, cilia have been recruited to perform additional developmental and homeostatic roles. Here, we review advances in deciphering the functional components of cilia, and we explore emerging trends that implicate ciliary proteins in signal transduction and morphogenetic pathways.
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Affiliation(s)
- Erica E Davis
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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376
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