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O'Hagan R, Avrutis A, Ramicevic E. Functions of the tubulin code in the C. elegans nervous system. Mol Cell Neurosci 2022; 123:103790. [PMID: 36368428 DOI: 10.1016/j.mcn.2022.103790] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 10/27/2022] [Accepted: 11/03/2022] [Indexed: 11/11/2022] Open
Abstract
Due to their elongated and polarized morphology, neurons rely on the microtubule (MT) cytoskeleton for their shape, as well as for efficient intracellular transport that maintains neuronal function, survival, and connectivity. Although all MTs are constructed from α- and β-tubulins that are highly conserved throughout eukaryotes, different MT networks within neurons exhibit different dynamics and functions. For example, molecular motors must be able to differentially recognize the axonal and dendritic MTs to deliver appropriate cargos to sensory endings and synaptic regions. The Tubulin Code hypothesis proposes that MTs can be specialized in form and function by chemical differences in their composition by inclusion of different α- and β-tubulins into the MT lattice, as well as differences in post-translational enzymatic modifications. The chemical differences encode information that allow MTs to regulate interactions with various microtubule-based molecular motors such as kinesins and dyneins as well as with structural microtubule-associated proteins (MAPs), which can, in turn, modify the function or stability of MTs. Here, we review studies involving C. elegans, a model organism with a relatively simple nervous system that is amenable to genetic analysis, that have contributed to our understanding of how the Tubulin Code can specialize neuronal MT networks to establish differences in neuronal morphology and function. Such studies have revealed molecules and mechanisms that are conserved in vertebrates and have the potential to inform our understanding of neurological diseases involving defects in the cytoskeleton and intracellular transport.
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Affiliation(s)
- Robert O'Hagan
- formerly at Biology Dept., Montclair State University, Montclair, NJ 07043, United States of America.
| | - Alexandra Avrutis
- formerly at Biology Dept., Montclair State University, Montclair, NJ 07043, United States of America
| | - Ema Ramicevic
- formerly at Biology Dept., Montclair State University, Montclair, NJ 07043, United States of America
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2
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Lu YM, Zheng C. The Expression and Function of Tubulin Isotypes in Caenorhabditis elegans. Front Cell Dev Biol 2022; 10:860065. [PMID: 35399537 PMCID: PMC8987236 DOI: 10.3389/fcell.2022.860065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 02/28/2022] [Indexed: 11/13/2022] Open
Abstract
Microtubules, made from the polymerization of the highly conserved α/β-tubulin heterodimers, serve as important components of the cytoskeleton in all eukaryotic cells. The existence of multiple tubulin isotypes in metazoan genomes and a dazzling variety of tubulin posttranslational modifications (PTMs) prompted the “tubulin code” hypothesis, which proposed that microtubule structure and functions are determined by the tubulin composition and PTMs. Evidence for the tubulin code has emerged from studies in several organisms with the characterization of specific tubulins for their expression and functions. The studies of tubulin PTMs are accelerated by the discovery of the enzymes that add or remove the PTMs. In tubulin research, the use of simple organisms, such as Caenorhabditis elegans, has been instrumental for understanding the expression and functional specialization of tubulin isotypes and the effects of their PTMs. In this review, we summarize the current understanding of the expression patterns and cellular functions of the nine α-tubulin and six β-tubulin isotypes. Expression studies are greatly facilitated by the CRISPR/Cas9-mediated endogenous GFP knock-in reporters and the organism-wide single cell transcriptomic studies. Meanwhile, functional studies benefit from the ease of genetic manipulation and precise gene replacement in C. elegans. These studies identified both ubiquitously expressed tubulin isotypes and tissue-specific isotypes. The isotypes showed functional redundancy, as well as functional specificity, which is likely caused by the subtle differences in their amino acid sequences. Many of these differences concentrate at the C-terminal tails that are subjected to several PTMs. Indeed, tubulin PTM, such as polyglutamylation, is shown to modulate microtubule organization and properties in both ciliated and non-ciliated neurons. Overall, studies from C. elegans support the distinct expression and function patterns of tubulin isotypes and the importance of their PTMs and offer the promise of cracking the tubulin code at the whole-genome and the whole-organism level.
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3
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Nishida K, Tsuchiya K, Obinata H, Onodera S, Honda Y, Lai YC, Haruta N, Sugimoto A. Expression Patterns and Levels of All Tubulin Isotypes Analyzed in GFP Knock-In C. elegans Strains. Cell Struct Funct 2021; 46:51-64. [PMID: 33967119 PMCID: PMC10511039 DOI: 10.1247/csf.21022] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 04/28/2021] [Indexed: 11/11/2022] Open
Abstract
Most organisms have multiple α- and β-tubulin isotypes that likely contribute to the diversity of microtubule (MT) functions. To understand the functional differences of tubulin isotypes in Caenorhabditis elegans, which has nine α-tubulin isotypes and six β-tubulin isotypes, we systematically constructed null mutants and GFP-fusion strains for all tubulin isotypes with the CRISPR/Cas9 system and analyzed their expression patterns and levels in adult hermaphrodites. Four isotypes-α-tubulins TBA-1 and TBA-2 and β-tubulins TBB-1 and TBB-2-were expressed in virtually all tissues, with a distinct tissue-specific spectrum. Other isotypes were expressed in specific tissues or cell types at significantly lower levels than the broadly expressed isotypes. Four isotypes (TBA-5, TBA-6, TBA-9, and TBB-4) were expressed in different subsets of ciliated sensory neurons, and TBB-4 was inefficiently incorporated into mitotic spindle MTs. Taken together, we propose that MTs in C. elegans are mainly composed of four broadly expressed tubulin isotypes and that incorporation of a small amount of tissue-specific isotypes may contribute to tissue-specific MT properties. These newly constructed strains will be useful for further elucidating the distinct roles of tubulin isotypes.Key words: tubulin isotypes, microtubules, C. elegans.
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Affiliation(s)
- Kei Nishida
- Laboratory of Developmental Dynamics, Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan
| | - Kenta Tsuchiya
- Laboratory of Developmental Dynamics, Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan
| | - Hiroyuki Obinata
- Laboratory of Developmental Dynamics, Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan
| | - Shizuka Onodera
- Laboratory of Developmental Dynamics, Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan
| | - Yu Honda
- Laboratory of Developmental Dynamics, Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan
| | - Yen-Cheng Lai
- Laboratory of Developmental Dynamics, Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan
| | - Nami Haruta
- Laboratory of Developmental Dynamics, Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan
| | - Asako Sugimoto
- Laboratory of Developmental Dynamics, Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan
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4
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How Caenorhabditis elegans Senses Mechanical Stress, Temperature, and Other Physical Stimuli. Genetics 2019; 212:25-51. [PMID: 31053616 PMCID: PMC6499529 DOI: 10.1534/genetics.118.300241] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 03/04/2019] [Indexed: 12/30/2022] Open
Abstract
Caenorhabditis elegans lives in a complex habitat in which they routinely experience large fluctuations in temperature, and encounter physical obstacles that vary in size and composition. Their habitat is shared by other nematodes, by beneficial and harmful bacteria, and nematode-trapping fungi. Not surprisingly, these nematodes can detect and discriminate among diverse environmental cues, and exhibit sensory-evoked behaviors that are readily quantifiable in the laboratory at high resolution. Their ability to perform these behaviors depends on <100 sensory neurons, and this compact sensory nervous system together with powerful molecular genetic tools has allowed individual neuron types to be linked to specific sensory responses. Here, we describe the sensory neurons and molecules that enable C. elegans to sense and respond to physical stimuli. We focus primarily on the pathways that allow sensation of mechanical and thermal stimuli, and briefly consider this animal’s ability to sense magnetic and electrical fields, light, and relative humidity. As the study of sensory transduction is critically dependent upon the techniques for stimulus delivery, we also include a section on appropriate laboratory methods for such studies. This chapter summarizes current knowledge about the sensitivity and response dynamics of individual classes of C. elegans mechano- and thermosensory neurons from in vivo calcium imaging and whole-cell patch-clamp electrophysiology studies. We also describe the roles of conserved molecules and signaling pathways in mediating the remarkably sensitive responses of these nematodes to mechanical and thermal cues. These studies have shown that the protein partners that form mechanotransduction channels are drawn from multiple superfamilies of ion channel proteins, and that signal transduction pathways responsible for temperature sensing in C. elegans share many features with those responsible for phototransduction in vertebrates.
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5
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Zheng C, Diaz-Cuadros M, Nguyen KCQ, Hall DH, Chalfie M. Distinct effects of tubulin isotype mutations on neurite growth in Caenorhabditis elegans. Mol Biol Cell 2017; 28:2786-2801. [PMID: 28835377 PMCID: PMC5638583 DOI: 10.1091/mbc.e17-06-0424] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 08/15/2017] [Accepted: 08/16/2017] [Indexed: 12/20/2022] Open
Abstract
Different tubulin isotypes perform different functions in the regulation of microtubule (MT) structure and neurite growth, and missense mutations of tubulin genes have three types of distinct effects on MT stability and neurite growth. One α-tubulin isotype appears to induce relative instability due to the lack of potential posttranslational modification sites. Tubulins, the building block of microtubules (MTs), play a critical role in both supporting and regulating neurite growth. Eukaryotic genomes contain multiple tubulin isotypes, and their missense mutations cause a range of neurodevelopmental defects. Using the Caenorhabditis elegans touch receptor neurons, we analyzed the effects of 67 tubulin missense mutations on neurite growth. Three types of mutations emerged: 1) loss-of-function mutations, which cause mild defects in neurite growth; 2) antimorphic mutations, which map to the GTP binding site and intradimer and interdimer interfaces, significantly reduce MT stability, and cause severe neurite growth defects; and 3) neomorphic mutations, which map to the exterior surface, increase MT stability, and cause ectopic neurite growth. Structure-function analysis reveals a causal relationship between tubulin structure and MT stability. This stability affects neuronal morphogenesis. As part of this analysis, we engineered several disease-associated human tubulin mutations into C. elegans genes and examined their impact on neuronal development at the cellular level. We also discovered an α-tubulin (TBA-7) that appears to destabilize MTs. Loss of TBA-7 led to the formation of hyperstable MTs and the generation of ectopic neurites; the lack of potential sites for polyamination and polyglutamination on TBA-7 may be responsible for this destabilization.
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Affiliation(s)
- Chaogu Zheng
- Department of Biological Sciences, Columbia University, New York, NY 10027
| | | | - Ken C Q Nguyen
- Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461
| | - David H Hall
- Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461
| | - Martin Chalfie
- Department of Biological Sciences, Columbia University, New York, NY 10027
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6
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Differential regulation of polarized synaptic vesicle trafficking and synapse stability in neural circuit rewiring in Caenorhabditis elegans. PLoS Genet 2017. [PMID: 28636662 PMCID: PMC5500376 DOI: 10.1371/journal.pgen.1006844] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Neural circuits are dynamic, with activity-dependent changes in synapse density and connectivity peaking during different phases of animal development. In C. elegans, young larvae form mature motor circuits through a dramatic switch in GABAergic neuron connectivity, by concomitant elimination of existing synapses and formation of new synapses that are maintained throughout adulthood. We have previously shown that an increase in microtubule dynamics during motor circuit rewiring facilitates new synapse formation. Here, we further investigate cellular control of circuit rewiring through the analysis of mutants obtained in a forward genetic screen. Using live imaging, we characterize novel mutations that alter cargo binding in the dynein motor complex and enhance anterograde synaptic vesicle movement during remodeling, providing in vivo evidence for the tug-of-war between kinesin and dynein in fast axonal transport. We also find that a casein kinase homolog, TTBK-3, inhibits stabilization of nascent synapses in their new locations, a previously unexplored facet of structural plasticity of synapses. Our study delineates temporally distinct signaling pathways that are required for effective neural circuit refinement. In this study, we identify pathways that regulate the formation and maintenance of synapses, the functional connections between neurons, in the nervous system of the nematode C. elegans. Our work characterizes the interaction between molecular motors kinesin and dynein, which carry cargo and move towards opposite ends of microtubules during synapse formation. We also address the role of a protein kinase gene TTBK-3 in maintaining synapse structure once synaptic components have reached the sites of new synapses. Our findings shed mechanistic insight into the coordination of molecular motors and the cytoskeleton in neural circuit function.
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7
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Lockhead D, Schwarz EM, O'Hagan R, Bellotti S, Krieg M, Barr MM, Dunn AR, Sternberg PW, Goodman MB. The tubulin repertoire of C. elegans sensory neurons and its context-dependent role in process outgrowth. Mol Biol Cell 2016; 27:mbc.E16-06-0473. [PMID: 27654945 PMCID: PMC5170555 DOI: 10.1091/mbc.e16-06-0473] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 09/12/2016] [Accepted: 09/15/2016] [Indexed: 12/21/2022] Open
Abstract
Microtubules contribute to many cellular processes, including transport, signaling, and chromosome separation during cell division (Kapitein and Hoogenraad, 2015). They are comprised of αβ-tubulin heterodimers arranged into linear protofilaments and assembled into tubes. Eukaryotes express multiple tubulin isoforms (Gogonea et al., 1999), and there has been a longstanding debate as to whether the isoforms are redundant or perform specialized roles as part of a tubulin code (Fulton and Simpson, 1976). Here, we use the well-characterized touch receptor neurons (TRNs) of Caenorhabditis elegans to investigate this question, through genetic dissection of process outgrowth both in vivo and in vitro With single-cell RNA-seq, we compare transcription profiles for TRNs with those of two other sensory neurons, and present evidence that each sensory neuron expresses a distinct palette of tubulin genes. In the TRNs, we analyze process outgrowth and show that four tubulins (tba-1, tba-2, tbb-1, and tbb-2) function partially or fully redundantly, while two others (mec-7 and mec-12) perform specialized, context-dependent roles. Our findings support a model in which sensory neurons express overlapping subsets of tubulin genes whose functional redundancy varies between cell types and in vivo and in vitro contexts.
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Affiliation(s)
- Dean Lockhead
- *Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305
| | - Erich M Schwarz
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853
| | - Robert O'Hagan
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854
| | - Sebastian Bellotti
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854
| | - Michael Krieg
- *Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305
| | - Maureen M Barr
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854
| | - Alexander R Dunn
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305 Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305
| | - Paul W Sternberg
- Howard Hughes Medical Institute and Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Miriam B Goodman
- *Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305
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8
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Abdus-Saboor I, Stone CE, Murray JI, Sundaram MV. The Nkx5/HMX homeodomain protein MLS-2 is required for proper tube cell shape in the C. elegans excretory system. Dev Biol 2012; 366:298-307. [PMID: 22537498 DOI: 10.1016/j.ydbio.2012.03.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Revised: 03/26/2012] [Accepted: 03/28/2012] [Indexed: 01/20/2023]
Abstract
Cells perform wide varieties of functions that are facilitated, in part, by adopting unique shapes. Many of the genes and pathways that promote cell fate specification have been elucidated. However, relatively few transcription factors have been identified that promote shape acquisition after fate specification. Here we show that the Nkx5/HMX homeodomain protein MLS-2 is required for cellular elongation and shape maintenance of two tubular epithelial cells in the C. elegans excretory system, the duct and pore cells. The Nkx5/HMX family is highly conserved from sea urchins to humans, with known roles in neuronal and glial development. MLS-2 is expressed in the duct and pore, and defects in mls-2 mutants first arise when the duct and pore normally adopt unique shapes. MLS-2 cooperates with the EGF-Ras-ERK pathway to turn on the LIN-48/Ovo transcription factor in the duct cell during morphogenesis. These results reveal a novel interaction between the Nkx5/HMX family and the EGF-Ras pathway and implicate a transcription factor, MLS-2, as a regulator of cell shape.
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Affiliation(s)
- Ishmail Abdus-Saboor
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
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9
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Motor neuron synapse and axon defects in a C. elegans alpha-tubulin mutant. PLoS One 2010; 5:e9655. [PMID: 20300184 PMCID: PMC2836382 DOI: 10.1371/journal.pone.0009655] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2009] [Accepted: 02/02/2010] [Indexed: 12/03/2022] Open
Abstract
Regulation of microtubule dynamics underlies many fundamental cellular mechanisms including cell division, cell motility, and transport. In neurons, microtubules play key roles in cell migration, axon outgrowth, control of axon and synapse growth, and the regulated transport of vesicles and structural components of synapses. Loss of synapse and axon integrity and disruption of axon transport characterize many neurodegenerative diseases. Recently, mutations that specifically alter the assembly or stability of microtubules have been found to directly cause neurodevelopmental defects or neurodegeneration in vertebrates. We report here the characterization of a missense mutation in the C-terminal domain of C. elegans alpha-tubulin, tba-1(ju89), that disrupts motor neuron synapse and axon development. Mutant ju89 animals exhibit reduction in the number and size of neuromuscular synapses, altered locomotion, and defects in axon extension. Although null mutations of tba-1 show a nearly wild-type pattern, similar axon outgrowth defects were observed in animals lacking the beta-tubulin TBB-2. Genetic analysis reveals that tba-1(ju89) affects synapse development independent of its role in axon outgrowth. tba-1(ju89) is an altered function allele that most likely perturbs interactions between TBA-1 and specific microtubule-associated proteins that control microtubule dynamics and transport of components needed for synapse and axon growth.
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Phillips JB, Lyczak R, Ellis GC, Bowerman B. Roles for two partially redundant alpha-tubulins during mitosis in early Caenorhabditis elegans embryos. ACTA ACUST UNITED AC 2005; 58:112-26. [PMID: 15083533 DOI: 10.1002/cm.20003] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The Caenorhabditis elegans genome encodes multiple isotypes of alpha-tubulin and beta-tubulin. Roles for a number of these tubulins in neuronal development have been described, but less is known about the isoforms that function during early embryonic development. Microtubules are required for multiple events after fertilization produces a one-cell zygote in C. elegans, including pronuclear migration, mitotic spindle assembly and function, and proper spindle positioning. Here we describe a conditional and dominant mis-sense mutation in the C. elegans alpha-tubulin gene tba-1 that disrupts pronuclear migration and positioning of the first mitotic spindle, and results in a highly penetrant embryonic lethality, at the restrictive temperature of 26 degrees C. Our analysis of the dominant tba-1 (or346ts) allele suggests that TBA-1 assembles into microtubules in early embryonic cells. However, we also show that reduction of tba-1 function using RNA interference results in defects much less severe than those caused by the dominant or346ts mutation, due to partial redundancy of TBA-1 and another alpha-tubulin called TBA-2. Reducing the function of both TBA-1 and TBA-2 results in severe defects in microtubule-dependent processes. We conclude that microtubules in the early C. elegans embryo are composed of both TBA-1 and TBA-2, and that the dominant tba-1(or346ts) mutation disrupts MT assembly or stability. Cell Motil.
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11
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Yang HY, McNally K, McNally FJ. MEI-1/katanin is required for translocation of the meiosis I spindle to the oocyte cortex in C elegans. Dev Biol 2003; 260:245-59. [PMID: 12885567 DOI: 10.1016/s0012-1606(03)00216-1] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
In most animals, successful segregation of female meiotic chromosomes involves sequential associations of the meiosis I and meiosis II spindles with the cell cortex so that extra chromosomes can be deposited in polar bodies. The resulting reduction in chromosome number is essential to prevent the generation of polyploid embryos after fertilization. Using time-lapse imaging of living Caenorhabditis elegans oocytes containing fluorescently labeled chromosomes or microtubules, we have characterized the movements of meiotic spindles relative to the cell cortex. Spindle assembly initiated several microns from the cortex. After formation of a bipolar structure, the meiosis I spindle translocated to the cortex. When microtubules were partially depleted, translocation of the bivalent chromosomes to the cortex was blocked without affecting cell cycle timing. In oocytes depleted of the microtubule-severing enzyme, MEI-1, spindles moved to the cortex, but association with the cortex was unstable. Unlike translocation of wild-type spindles, movement of MEI-1-depleted spindles was dependent on FZY-1/CDC20, a regulator of the metaphase/anaphase transition. We observed a microtubule and FZY-1/CDC20-dependent circular cytoplasmic streaming in wild-type and mei-1 mutant embryos during meiosis. We propose that, in mei-1 mutant oocytes, this cytoplasmic streaming is sufficient to drive the spindle into the cortex. Cytoplasmic streaming is not the normal spindle translocation mechanism because translocation occurred in the absence of cytoplasmic streaming in embryos depleted of either the orbit/CLASP homolog, CLS-2, or FZY-1. These results indicate a direct role of microtubule severing in translocation of the meiotic spindle to the cortex.
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Affiliation(s)
- Hsin-ya Yang
- Section of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA
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12
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Sly BJ, Hazel JC, Popodi EM, Raff RA. Patterns of gene expression in the developing adult sea urchin central nervous system reveal multiple domains and deep-seated neural pentamery. Evol Dev 2002; 4:189-204. [PMID: 12054292 DOI: 10.1046/j.1525-142x.2002.02002.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The adult sea urchin central nervous system (CNS) is composed of five radial nerve cords connected to a circular nerve ring. Although much is known about the molecular mechanisms underlying the development and function of the nervous systems of many invertebrate and vertebrate species, virtually nothing is known about these processes in echinoderms. We have isolated a set of clones from a size-selected cDNA library prepared from the nervous system of the sea urchin Heliocidaris erythrogramma for use as probes. A total of 117 expressed sequence clones were used to search the GenBank database. Identified messages include genes that encode signaling proteins, cytoskeletal elements, cell surface proteins and receptors, cell proliferation and differentiation factors, transport and channel proteins, and a RNA DEAD box helicase. Expression was analyzed by RNA gel blot hybridization to document expression through development. Many of the genes have apparently neural limited expression and function, but some have been co-opted into new roles, notably associated with exocytotic events at fertilization. Localization of gene expression by whole-mount in situ hybridization shows that the morphologically simple sea urchin radial CNS exhibits complex organization into localized transcriptional domains. The transcription patterns reflect the morphological pentamery of the echinoderm CNS and provide no indication of an underlying functional bilateral symmetry in the CNS.
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Affiliation(s)
- Belinda J Sly
- Indiana Molecular Biology Institute and Department of Biology, Indiana University, Bloomington 47405, USA
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13
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Abstract
In eukaryotic cells members of the kinesin family mediate intracellular transport by carrying cellular cargo on microtubule tracks. The nematode Caenorhabditis elegans genome encodes 21 members of the kinesin family, which show significant homology to their mammalian orthologs. Based on motor domain sequence homology and placement of the motor domain in the protein, the C. elegans kinesins have been placed in eight distinct groups; members of which participate in embryonic development, protein transport, synaptic membrane vesicles movement and in the axonal growth. Among 21 kinesins, at least 11 play a central role in spindle movement and chromosomal segregation. Understanding the function of C. elegans kinesins and related proteins may help navigate through the intricacies of intracellular traffic in a simple animal.
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Affiliation(s)
- Shahid S Siddiqui
- Pharmacology Department, M/C 867, College of Medicine, University of Illinois, Chicago, IL 60607, USA.
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14
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Baleanu-Gogonea C, Siddiqui SS. Molecular cloning and three-dimensional structure prediction of a novel alpha-tubulin in Caenorhabditis elegans. J Cell Mol Med 2000; 4:183-195. [PMID: 12167287 PMCID: PMC6741322 DOI: 10.1111/j.1582-4934.2000.tb00116.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
This paper reports on the isolation of a cDNA clone (tba-6) encoded by a novel alpha-tubulin gene in the nematode C. elegans. The tba-6 gene is located on chromosome I, that encode a protein of 460 amino acids, as well as the expression of the gene during the development. Here we discuss the structure of the coding region and the regulatory sequences in the promoter region. The comparison of the amino acid sequence of TBA6 with other alpha-tubulin isotypes of C. elegans, suggests that these proteins are highly conserved in most of the N-terminal and intermediate sequence, but they have highly divergent C-terminal sequences. TBA6 has also high homology with other alpha-tubulin families (e.g. human, mouse, Drosophila melangaster). The in situ experiment results suggest that the tba-6 alpha-tubulin gene is required during the entire embryonic development, therefore it is required during the early cell division stages. Further, we determined the 3D structure of C. elegans TBA6 alpha-tubulin by altering (computationally) the crystal structure of the alpha-tubulin (TBA_pig) from porcine alpha- beta tubulin dimer. We discuss structural conservation and changes in the pattern of interactions between secondary structure elements of TBA_pig and TBA6, respectively.
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Affiliation(s)
- Camelia Baleanu-Gogonea
- 331 South Frear Lab., Dept. Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA.
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15
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Gogonea CB, Gogonea V, Ali YM, Merz KM, Siddiqui SS. Computational prediction of the three-dimensional structures for the Caenorhabditis elegans tubulin family. J Mol Graph Model 1999; 17:90-100, 126-30. [PMID: 10680114 DOI: 10.1016/s1093-3263(99)00025-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
In this article we characterize, from a structural point of view, all 16 members of the tubulin gene family of Caenorhabditis elegans (9 alpha-tubulins, 6 beta-tubulins, and 1 gamma-tubulin). We obtained their tertiary structures by computationally modifying the X-ray crystal structure of the pig brain alpha/beta-tubulin dimer published by Nogales et al. [Nature (London) 1998;391:199-203]. Our computational protocol involves changing the amino acids (with MIDAS; Jarvis et al., UCSF MIDAS. University of California, San Francisco, 1986) in the 3D structure of pig brain alpha/beta-tubulin dimer followed by geometry optimization with the AMBER force field (Perlman et al., AMBER 4. University of California, San Francisco, 1990). We subsequently analyze and compare the resulting structures in terms of the differences in their secondary and tertiary structures. In addition, we compare the pattern of hydrogen bonds and hydrophobic contacts in the guanosine triphosphate (GTP)-binding site for all members of the tubulin family. Our computational results show that, except for gamma-tubulin, all members of the C. elegans tubulin family have similar secondary and 3D structures and that the change in the pattern of hydrogen bonds in the GTP-binding site may be used to assess the relative stability of different alpha/beta-tubulin dimers formed by monomers of the tubulin family.
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Affiliation(s)
- C B Gogonea
- Department of Ecological Engineering, Toyohashi University of Technology, Japan
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16
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Fedorov A, Johnston H, Korneev S, Blackshaw S, Davies J. Cloning, characterisation and expression of the alpha-tubulin genes of the leech, Hirudo medicinalis. Gene 1999; 227:11-9. [PMID: 9931409 DOI: 10.1016/s0378-1119(98)00603-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
We have isolated two alpha-tubulin cDNAs from the leech, Hirudo medicinalis. Both encode putative proteins of 451 amino-acids which differ from each other at only two positions. Southern blotting suggests that there are only two alpha-tubulin genes in the leech. The genes contain two introns and, because of the extremely high homology of the nucleotide sequence from the second intron to the end of the genes, we have inferred that a gene conversion event about 9.5 million years ago has homogenised the Hirudo alpha-tubulin sequences. Using in situ hybridisation to tissue sections, we have shown that the two genes are probably expressed in all neurons of the leech ganglia and that their spatial distribution remains unchanged during neuronal regeneration. The deduced amino-acid sequences of the leech alpha-tubulins show that they have greatest similarity to those from a platyhelminth, echiuran and mollusc with rather less to arthropod alpha-tubulins. The protein sequences of the leech alpha-tubulins have been compared with representatives of those from across all phyla to determine if any specific feature labels certain isotypes of tubulin for neuronal expression.
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Affiliation(s)
- A Fedorov
- Sussex Centre for Neuroscience, Sussex University, Falmer, Brighton BN1 9QG, UK
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17
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Ludueña RF. Multiple forms of tubulin: different gene products and covalent modifications. INTERNATIONAL REVIEW OF CYTOLOGY 1997; 178:207-75. [PMID: 9348671 DOI: 10.1016/s0074-7696(08)62138-5] [Citation(s) in RCA: 428] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Tubulin, the subunit protein of microtubules, is an alpha/beta heterodimer. In many organisms, both alpha and beta exist in numerous isotypic forms encoded by different genes. In addition, both alpha and beta undergo a variety of posttranslational covalent modifications, including acetylation, phosphorylation, detyrosylation, polyglutamylation, and polyglycylation. In this review the distribution and possible functional significance of the various forms of tubulin are discussed. In analyzing the differences among tubulin isotypes encoded by different genes, some appear to have no functional significance, some increase the overall adaptability of the organism to environmental challenges, and some appear to perform specific functions including formation of particular organelles and interactions with specific proteins. Purified isotypes also display different properties in vitro. Although the significance of all the covalent modification of tubulin is not fully understood, some of them may influence the stability of modified microtubules in vivo as well as interactions with certain proteins and may help to determine the functional role of microtubules in the cell. The review also discusses isotypes of gamma-tubulin and puts various forms of tubulin in an evolutionary context.
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Affiliation(s)
- R F Ludueña
- Department of Biochemistry, University of Texas Health Science Center at San Antonio 78284, USA
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18
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Khan ML, Gogonea CB, Siddiqui ZK, Ali MY, Kikuno R, Nishikawa K, Siddiqui SS. Molecular cloning and expression of the Caenorhabditis elegans klp-3, an ortholog of C terminus motor kinesins Kar3 and ncd. J Mol Biol 1997; 270:627-39. [PMID: 9245592 DOI: 10.1006/jmbi.1997.1112] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Common to all eukaryotes, kinesins are cytoskeletal motor proteins that mediate intracellular transport on microtubule tracks, using ATP hydrolysis. A Caenorhabditis elegans cDNA clone corresponding to the klp-3 gene, encoding a novel kinesin, was isolated, and mapped on LGII. Northern blot analysis using the klp-3 cDNA probe reveals a 1.9 kb mRNA that is transcribed at a low level during development. Temporal and spatial expression of the klp-3::lacZ fusion gene is limited to the marginal cells in the pharynx, and a group of muscle cells in the posterior gut region. The nucleotide sequence of klp-3 has been deduced from the cDNA and nematode genome sequencing consortium data. Conceptual translation of the klp-3 gene reveals a kinesin-like protein with its conserved motor domain containing the ATP binding and microtubule binding sites located in the C terminus. KLP-3 shares extensive homology with the yeast Kar3 and Drosophila ncd kinesins, which have previously been shown to mediate chromosomal movement and segregation during meiosis and mitosis. Overexpression of the klp-3 gene partially rescues the lethal phenotype of the maternal lethal him-14 ts(it44) mutants at non-permissive temperatures, and reduces the incidence of males caused by non-disjunction of the X-chromosome. Similarly, expression of a klp-3 antisense RNA, under the control of a heat shock promoter, causes embryonic arrest, dead eggs and polyploid cells in transgenic lines, suggesting a critical role for the klp-3 function in chromosome segregation. Further analysis of the klp-3 gene in C. elegans may elucidate diverse functions of the C terminus mitotic motor proteins during development.
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Affiliation(s)
- M L Khan
- Laboratory of Molecular Biology, Department of Ecological Engineering, Toyohashi University of Technology, Toyohashi, 441, Japan
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19
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Fukushige T, Siddiqui SS. Effect of the dpy-20 and rol-6 cotransformation markers on alpha-tubulin gene expression in C. elegans transformants. Transgenic Res 1995; 4:332-40. [PMID: 8589736 DOI: 10.1007/bf01972530] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
An alpha-1 tubulin::lacZ fusion gene was introduced into the germline of Caenorhabditis elegans, using either rol-6 or dpy-20 genomic DNA as a cotransformation marker. Distinct patterns in cellular specificity of the alpha-1 tubulin::lacZ fusion gene expression were observed, depending on the cotransformation marker used. For the rol-6 marker, the tubulin fusion gene was expressed in several neurons in the head and tail ganglia and a set of 38-39 ventral cord motor neurons along the body length of the animal during larval and adult development. In contrast, for the dpy-20 marker system, not only were fewer neurons stained in the head and tail region, but also the staining of ventral cord motor neurons was extremely reduced both in number and intensity. The dpy-20 marked-mediated suppression of the alpha-1 tubulin gene expression was observed both in the cis and trans configurations. Similar down-regulation in the ventral cord motor neurons was observed when the alpha-2 tubulin::lacZ fusion gene construct was tested in these experiments using the dpy-20 marker. In controls, where the tubulin fusion gene was directly injected to obtain transformants without any marker DNA, the cellular staining pattern was close to the fusion gene expression observed with the rol-6 marker DNA. These results underline the importance of the choice of transformation marker system in generation of the transgenic animals, and reveal a down-regulation of the alpha-tubulin fusion gene expression in the ventral cord motor neurons in transgenic animals when the dpy-20 gene was used as a cotransformation marker.
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Affiliation(s)
- T Fukushige
- Department of Ecological Engineering, Toyohashi University of Technology, Japan
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