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Postlethwait JH, Yan YL, Desvignes T, Allard C, Titus T, Le François NR, Detrich HW. Embryogenesis and early skeletogenesis in the antarctic bullhead notothen, Notothenia coriiceps. Dev Dyn 2016; 245:1066-1080. [PMID: 27507212 DOI: 10.1002/dvdy.24437] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 07/01/2016] [Accepted: 07/04/2016] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Environmental temperature influences rates of embryonic development, but a detailed staging series for vertebrate embryos developing in the subzero cold of Antarctic waters is not yet available from fertilization to hatching. Given projected warming of the Southern Ocean, it is imperative to establish a baseline to evaluate potential effects of changing climate on fish developmental dynamics. RESULTS We studied the Bullhead notothen (Notothenia coriiceps), a notothenioid fish inhabiting waters between -1.9 and +2 °C. In vitro fertilization produced embryos that progressed through cleavage, epiboly, gastrulation, segmentation, organogenesis, and hatching. We compared morphogenesis spatially and temporally to Zebrafish and medaka. Experimental animals hatched after about 6 months to early larval stages. To help understand skeletogenesis, we analyzed late embryos for expression of sox9 and runx2, which regulate chondrogenesis, osteogenesis, and eye development. Results revealed that, despite their prolonged developmental time course, N. coriiceps embryos developed similarly to those of other teleosts with large yolk cells. CONCLUSIONS Our studies set the stage for future molecular analyses of development in these extremophile fish. Results provide a foundation for understanding the impact of ocean warming on embryonic development and larval recruitment of notothenioid fish, which are key factors in the marine trophic system. Developmental Dynamics 245:1066-1080, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
| | - Yi-Lin Yan
- Institute of Neuroscience, University of Oregon, Eugene, Oregon
| | | | - Corey Allard
- Biodôme de Montréal, Division des collections vivantes et recherche, Montréal, Quebec, Canada
| | - Tom Titus
- Institute of Neuroscience, University of Oregon, Eugene, Oregon
| | - Nathalie R Le François
- Department of Marine and Environmental Sciences, Marine Science Center, Northeastern University, Nahant, Massachusetts
| | - H William Detrich
- Biodôme de Montréal, Division des collections vivantes et recherche, Montréal, Quebec, Canada
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Beers JM, Jayasundara N. Antarctic notothenioid fish: what are the future consequences of 'losses' and 'gains' acquired during long-term evolution at cold and stable temperatures? ACTA ACUST UNITED AC 2016; 218:1834-45. [PMID: 26085661 DOI: 10.1242/jeb.116129] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Antarctic notothenioids dominate the fish fauna of the Southern Ocean. Evolution for millions of years at cold and stable temperatures has led to the acquisition of numerous biochemical traits that allow these fishes to thrive in sub-zero waters. The gain of antifreeze glycoproteins has afforded notothenioids the ability to avert freezing and survive at temperatures often hovering near the freezing point of seawater. Additionally, possession of cold-adapted proteins and membranes permits them to sustain appropriate metabolic rates at exceptionally low body temperatures. The notothenioid genome is also distinguished by the disappearance of traits in some species, losses that might prove costly in a warmer environment. Perhaps the best-illustrated example is the lack of expression of hemoglobin in white-blooded icefishes from the family Channichthyidae. Loss of key elements of the cellular stress response, notably the heat shock response, has also been observed. Along with their attainment of cold tolerance, notothenioids have developed an extreme stenothermy and many species perish at temperatures only a few degrees above their habitat temperatures. Thus, in light of today's rapidly changing climate, it is critical to evaluate how these extreme stenotherms will respond to rising ocean temperatures. It is conceivable that the remarkable cold specialization of notothenioids may ultimately leave them vulnerable to future thermal increases and threaten their fitness and survival. Within this context, our review provides a current summary of the biochemical losses and gains that are known for notothenioids and examines these cold-adapted traits with a focus on processes underlying thermal tolerance and acclimation capacity.
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Affiliation(s)
- Jody M Beers
- Hopkins Marine Station, Stanford University, 120 Ocean View Boulevard, Pacific Grove, CA 93950, USA
| | - Nishad Jayasundara
- Nicholas School of the Environment, Duke University, 450 Research Drive, Durham, NC 27708, USA
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Cuellar J, Yébenes H, Parker SK, Carranza G, Serna M, Valpuesta JM, Zabala JC, Detrich HW. Assisted protein folding at low temperature: evolutionary adaptation of the Antarctic fish chaperonin CCT and its client proteins. Biol Open 2014; 3:261-70. [PMID: 24659247 PMCID: PMC3988795 DOI: 10.1242/bio.20147427] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Eukaryotic ectotherms of the Southern Ocean face energetic challenges to protein folding assisted by the cytosolic chaperonin CCT. We hypothesize that CCT and its client proteins (CPs) have co-evolved molecular adaptations that facilitate CCT–CP interaction and the ATP-driven folding cycle at low temperature. To test this hypothesis, we compared the functional and structural properties of CCT–CP systems from testis tissues of an Antarctic fish, Gobionotothen gibberifrons (Lönnberg) (habitat/body T = −1.9 to +2°C), and of the cow (body T = 37°C). We examined the temperature dependence of the binding of denatured CPs (β-actin, β-tubulin) by fish and bovine CCTs, both in homologous and heterologous combinations and at temperatures between −4°C and 20°C, in a buffer conducive to binding of the denatured CP to the open conformation of CCT. In homologous combination, the percentage of G. gibberifrons CCT bound to CP declined linearly with increasing temperature, whereas the converse was true for bovine CCT. Binding of CCT to heterologous CPs was low, irrespective of temperature. When reactions were supplemented with ATP, G. gibberifrons CCT catalyzed the folding and release of actin at 2°C. The ATPase activity of apo-CCT from G. gibberifrons at 4°C was ∼2.5-fold greater than that of apo-bovine CCT, whereas equivalent activities were observed at 20°C. Based on these results, we conclude that the catalytic folding cycle of CCT from Antarctic fishes is partially compensated at their habitat temperature, probably by means of enhanced CP-binding affinity and increased flexibility of the CCT subunits.
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Affiliation(s)
- Jorge Cuellar
- Centro Nacional de Biotechnología (CNB-CSIC), Campus de la Universidad Autónoma de Madrid, 28049 Madrid, Spain
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Atomic water channel controlling remarkable properties of a single brain microtubule: correlating single protein to its supramolecular assembly. Biosens Bioelectron 2013; 47:141-8. [PMID: 23567633 DOI: 10.1016/j.bios.2013.02.050] [Citation(s) in RCA: 90] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Revised: 02/20/2013] [Accepted: 02/21/2013] [Indexed: 11/21/2022]
Abstract
Microtubule nanotubes are found in every living eukaryotic cells; these are formed by reversible polymerization of the tubulin protein, and their hollow fibers are filled with uniquely arranged water molecules. Here we measure single tubulin molecule and single brain-neuron extracted microtubule nanowire with and without water channel inside to unravel their unique electronic and optical properties for the first time. We demonstrate that the energy levels of a single tubulin protein and single microtubule made of 40,000 tubulin dimers are identical unlike conventional materials. Moreover, the transmitted ac power and the transient fluorescence decay (single photon count) are independent of the microtubule length. Even more remarkable is the fact that the microtubule nanowire is more conducting than a single protein molecule that constitutes the nanowire. Microtubule's vibrational peaks condense to a single mode that controls the emergence of size independent electronic/optical properties, and automated noise alleviation, which disappear when the atomic water core is released from the inner cylinder. We have carried out several tricky state-of-the-art experiments and identified the electromagnetic resonance peaks of single microtubule reliably. The resonant vibrations established that the condensation of energy levels and periodic oscillation of unique energy fringes on the microtubule surface, emerge as the atomic water core resonantly integrates all proteins around it such that the nanotube irrespective of its size functions like a single protein molecule. Thus, a monomolecular water channel residing inside the protein-cylinder displays an unprecedented control in governing the tantalizing electronic and optical properties of microtubule.
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Sahab ZJ, Kirilyuk A, Zhang L, Khamis ZI, Pompach P, Sung Y, Byers SW. Analysis of tubulin alpha-1A/1B C-terminal tail post-translational poly-glutamylation reveals novel modification sites. J Proteome Res 2012; 11:1913-23. [PMID: 22296162 PMCID: PMC3292626 DOI: 10.1021/pr2011044] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Tubulin-α(1A/1B) C-terminal tail (CTT) has seven glutamic acid residues among the last 11 amino acids of its sequence that are potential sites for glutamylation. Cleavage of C-terminal tyrosine resulting in the detyrosinated form of tubulin-α(1A/1B) is another major modification. These modifications among others bring about highly heterogeneous tubulin samples in brain cells and microtubules, play a major role in directing intracellular trafficking, microtubule dynamics, and mitotic events, and can vary depending on the cell and disease state, such as cancer and neurodegenerative disorders. Identified previously using primary mass spectrometry (MS) ions and partial Edman sequencing, tubulin-α(1A/1B) glutamylation was found exclusively on the E(445) residue. We here describe the analysis of tubulin-α(1A/1B) glutamylation and detyrosination after 2-DE separation, trypsin and proteinase K in-gel digestion, and nanoUPLC-ESI-QqTOF-MS/MS of mouse brain and bovine microtubules. Tyrosinated, detyrosinated, and Δ2-tubulin-α(1A/1B) CTTs were identified on the basis of a comparison of fragmentation patterns and retention times between endogenous and synthetic peptides. Stringent acceptance criteria were adapted for the identification of novel glutamylation sites. In addition to the previously identified site at E(445), glutamylation on mouse and bovine tubulin-α(1A/1B) CTTs was identified on E(441) and E(443) with MASCOT Expect values below 0.01. O-Methylation of glutamates was also observed.
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Affiliation(s)
- Ziad J Sahab
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University , Washington, DC 20007, United States.
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Giordano D, Russo R, di Prisco G, Verde C. Molecular adaptations in Antarctic fish and marine microorganisms. Mar Genomics 2011; 6:1-6. [PMID: 22578653 DOI: 10.1016/j.margen.2011.09.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2011] [Revised: 09/01/2011] [Accepted: 09/07/2011] [Indexed: 01/10/2023]
Abstract
The Antarctic marine environment is one of the most extreme on Earth due to its stably low temperature and high oxygen content. Here we discuss various aspects of the molecular adaptations evolved by Antarctic fish and marine microorganisms living in this environment. This review will in particular focus on: (i) the genetic/genomic bases of adaptation in Antarctic notothenioid fish; (ii) the role of neuroglobin recently identified in the brain of Antarctic icefish; (iii) the structural and functional features of globins of the Antarctic marine bacterium Pseudoalteromonas haloplanktis TAC125.
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Affiliation(s)
- Daniela Giordano
- Institute of Protein Biochemistry, CNR, Via Pietro Castellino 111, I-80131 Naples, Italy
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Rogowski K, van Dijk J, Magiera MM, Bosc C, Deloulme JC, Bosson A, Peris L, Gold ND, Lacroix B, Bosch Grau M, Bec N, Larroque C, Desagher S, Holzer M, Andrieux A, Moutin MJ, Janke C. A family of protein-deglutamylating enzymes associated with neurodegeneration. Cell 2010; 143:564-78. [PMID: 21074048 DOI: 10.1016/j.cell.2010.10.014] [Citation(s) in RCA: 257] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2010] [Revised: 08/13/2010] [Accepted: 10/05/2010] [Indexed: 12/11/2022]
Abstract
Polyglutamylation is a posttranslational modification that generates glutamate side chains on tubulins and other proteins. Although this modification has been shown to be reversible, little is known about the enzymes catalyzing deglutamylation. Here we describe the enzymatic mechanism of protein deglutamylation by members of the cytosolic carboxypeptidase (CCP) family. Three enzymes (CCP1, CCP4, and CCP6) catalyze the shortening of polyglutamate chains and a fourth (CCP5) specifically removes the branching point glutamates. In addition, CCP1, CCP4, and CCP6 also remove gene-encoded glutamates from the carboxyl termini of proteins. Accordingly, we show that these enzymes convert detyrosinated tubulin into Δ2-tubulin and also modify other substrates, including myosin light chain kinase 1. We further analyze Purkinje cell degeneration (pcd) mice that lack functional CCP1 and show that microtubule hyperglutamylation is directly linked to neurodegeneration. Taken together, our results reveal that controlling the length of the polyglutamate side chains on tubulin is critical for neuronal survival.
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Affiliation(s)
- Krzysztof Rogowski
- CRBM, Université Montpellier 2 and 1, CNRS UMR 5237, Montpellier 34293, France.
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8
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Giordano D, Russo R, Coppola D, di Prisco G, Verde C. Molecular adaptations in haemoglobins of notothenioid fishes. JOURNAL OF FISH BIOLOGY 2010; 76:301-318. [PMID: 20738709 DOI: 10.1111/j.1095-8649.2009.02528.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Since haemoglobins of all animal species have the same haem group, differences in their properties, including oxygen affinity, electrophoretic mobility and pH sensitivity, must result from the interaction of the prosthetic group with specific amino-acid residues in the primary structure. For this reason, fish globins have been the subject of extensive studies in recent years, not only for their structural characteristics, but also because they offer the possibility to investigate the evolutionary history of these ancient molecules in marine and freshwater species living in a great variety of environmental conditions. This review summarizes the current knowledge on the structure, function and phylogeny of haemoglobins of notothenioid fishes. On the basis of crystallographic analysis, the evolution of the Root effect is analysed. Adaptation of the oxygen transport system in notothenioids seems to be based on evolutionary changes, involving levels of biological organization higher than the structure of haemoglobin. These include changes in the rate of haemoglobin synthesis or in regulation by allosteric effectors, which affect the amount of oxygen transported in blood. These factors are thought to be more important for short-term response to environmental challenges than previously believed.
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Affiliation(s)
- D Giordano
- Institute of Protein Biochemistry, CNR, Via Pietro Castellino 111, I-80131 Naples, Italy
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9
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Redeker V. Mass spectrometry analysis of C-terminal posttranslational modifications of tubulins. Methods Cell Biol 2010; 95:77-103. [PMID: 20466131 DOI: 10.1016/s0091-679x(10)95006-1] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
In mammalian brain and ciliary axonemes from ciliates, alpha- and beta-tubulins exhibit an extraordinary heterogeneity due to a combination of multigene family expression and numerous posttranslational modifications (PTMs). The combination of several PTMs located in the C-terminal tail of tubulins plays a major role in this important polymorphism of tubulin: polyglutamylation, polyglycylation, detyrosination, tyrosination, removal of the penultimate glutamate residue, and phosphorylation. In order to document the relationship and functions of these PTMs, we have developed a tubulin C-terminal Peptide Mass Fingerprinting (PMF) method. Using simplified microtubule proteins and tubulin C-terminal peptides purifications, direct matrix-assisted laser desorption ionization (MALDI) mass spectrometry (MS) analysis can generate a complete picture of all tubulin isotype-specific C-terminal peptides together with their respective PTMs. This chapter will illustrate the capability of this approach to compare tubulin isoform compositions and document the changes in PTMs between samples with different tubulin assembly properties or consecutively to inactivation of modification sites or modification enzymes. Complementary MS-based approaches useful to document the structure of the highly heterogeneous posttranslational polymodifications will also be presented.
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Affiliation(s)
- Virginie Redeker
- Laboratoire d'Enzymologie et Biochimie Structurales, CNRS, 91198 Gif-sur-Yvette cedex, France
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10
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Abstract
Tubulin antibodies are among the most extensively used immunological reagents in basic and applied cell and molecular biology. In this chapter, we provide a brief overview of the practices and reagents developed in our laboratory during the past 25 years for characterizing anti-beta-tubulin antibodies.
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Affiliation(s)
- Anthony J Spano
- Department of Biology, University of Virginia, Charlottesville, Virginia 22904, USA
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11
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Pucciarelli S, La Terza A, Ballarini P, Barchetta S, Yu T, Marziale F, Passini V, Methé B, Detrich HW, Miceli C. Molecular cold-adaptation of protein function and gene regulation: The case for comparative genomic analyses in marine ciliated protozoa. Mar Genomics 2009; 2:57-66. [PMID: 21798173 DOI: 10.1016/j.margen.2009.03.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2008] [Revised: 03/16/2009] [Accepted: 03/25/2009] [Indexed: 12/01/2022]
Abstract
Euplotes focardii is a marine ciliated protozoan discovered in the Ross Sea near Terra Nova Bay, Antarctica. This organism is strictly psychrophilic, survives and reproduces optimally at 4-5 °C, and has a genome rich in A/T base pairs. Like other ciliated protozoans, Euplotes spp. are characterized by nuclear dimorphism: 1) the germline micronucleus contains the entire genome as large chromosomes; and 2) the somatic macronucleus (∼50 megabases, or 5% of the micronuclear genome) contains small linear DNA nanochromosomes [1-12 kilobases], each of which constitutes a single genetic unit. These characteristics make E. focardii an ideal model for genome-level analysis to understand the evolutionary mechanisms that determine the adaptation of organisms to cold environments. Here we describe two examples that are controlled by phylogenetically appropriate comparison with mesophilic and psychrotolerant Euplotes species: 1) the genes and encoded proteins of the E. focardii tubulin superfamily, including α-, β-, and γ-tubulins; and 2) the genes of the heat-shock protein (Hsp) 70 family. The tubulins provide particular insight into protein-level structural changes that are likely to facilitate microtubule nucleation and polymerization in an energy poor environment. By contrast, the hsp70 genes of E. focardii and of its psychrotolerant relative E. nobilii reveal adaptive alterations in the regulation of gene expression in the cold. The unique characteristics of the E. focardii genome and the results that we present here argue strongly for a concerted effort to characterize the relatively low complexity macronuclear genome of this psychrophilic organism.
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Affiliation(s)
- Sandra Pucciarelli
- Dipartimento di Biologia Molecolare, Cellulare, Animale, University of Camerino, Camerino (MC), Italy
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12
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Marziale F, Pucciarelli S, Ballarini P, Melki R, Uzun A, Ilyin VA, Detrich HW, Miceli C. Different roles of two gamma-tubulin isotypes in the cytoskeleton of the Antarctic ciliate Euplotes focardii: remodelling of interaction surfaces may enhance microtubule nucleation at low temperature. FEBS J 2008; 275:5367-82. [PMID: 18959762 DOI: 10.1111/j.1742-4658.2008.06666.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Gamma-tubulin belongs to the tubulin superfamily and plays an essential role in the nucleation of cellular microtubules. In the present study, we report the characterization of gamma-tubulin from the psychrophilic Antarctic ciliate Euplotes focardii. In this organism, gamma-tubulin is encoded by two genes, gamma-T1 and gamma-T2, that produce distinct isotypes. Comparison of the gamma-T1 and gamma-T2 primary sequences to a Euplotesgamma-tubulin consensus, derived from mesophilic (i.e. temperate) congeneric species, revealed the presence of numerous unique amino acid substitutions, particularly in gamma-T2. Structural models of gamma-T1 and gamma-T2, obtained using the 3D structure of human gamma-tubulin as a template, suggest that these substitutions are responsible for conformational and/or polarity differences located: (a) in the regions involved in longitudinal 'plus end' contacts; (b) in the T3 loop that participates in binding GTP; and (c) in the M loop that forms lateral interactions. Relative to gamma-T1, the gamma-T2 gene is amplified by approximately 18-fold in the macronuclear genome and is very strongly transcribed. Using confocal immunofluorescence microscopy, we found that the gamma-tubulins of E. focardii associate throughout the cell cycle with basal bodies of the non-motile dorsal cilia and of all of the cirri of the ventral surface (i.e. adoral membranelles, paraoral membrane, and frontoventral transverse, caudal and marginal cirri). By contrast, only gamma-T2 interacts with the centrosomes of the spindle during micronuclear mitosis. We also established that the gamma-T1 isotype associates only with basal bodies. Our results suggest that gamma-T1 and gamma-T2 perform different functions in the organization of the microtubule cytoskeleton of this protist and are consistent with the hypothesis that gamma-T1 and gamma-T2 have evolved sequence-based structural alterations that facilitate template nucleation of microtubules by the gamma-tubulin ring complex at cold temperatures.
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Affiliation(s)
- Francesca Marziale
- Dipartimento di Biologia Molecolare, Cellulare e Animale, University of Camerino, Italy
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Tartaglia LJ, Shain DH. Cold-adapted tubulins in the glacier ice worm, Mesenchytraeus solifugus. Gene 2008; 423:135-41. [DOI: 10.1016/j.gene.2008.07.025] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2007] [Revised: 07/04/2008] [Accepted: 07/18/2008] [Indexed: 01/02/2023]
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Verdier-Pinard P, Pasquier E, Xiao H, Burd B, Villard C, Lafitte D, Miller LM, Angeletti RH, Horwitz SB, Braguer D. Tubulin proteomics: towards breaking the code. Anal Biochem 2008; 384:197-206. [PMID: 18840397 DOI: 10.1016/j.ab.2008.09.020] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2008] [Revised: 09/12/2008] [Accepted: 09/15/2008] [Indexed: 01/02/2023]
Affiliation(s)
- Pascal Verdier-Pinard
- INSERM UMR 911 CRO2, Aix-Marseille Université, Faculté de Pharmacie, 27 bd Jean Moulin, 13285 Marseille cedex 05, France.
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15
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Olson MT, Blank PS, Sackett DL, Yergey AL. Evaluating reproducibility and similarity of mass and intensity data in complex spectra--applications to tubulin. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2008; 19:367-374. [PMID: 18207417 DOI: 10.1016/j.jasms.2007.11.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2007] [Revised: 11/06/2007] [Accepted: 11/07/2007] [Indexed: 05/25/2023]
Abstract
We present a data processing approach based on the spectral dot product for evaluating spectral similarity and reproducibility. The method introduces 95% confidence intervals on the spectral dot product to evaluate the strength of spectral correlation; it is the only calculation described to date that accounts for both the non-normal sampling distribution of the dot product and the number of peaks the spectra have in common. These measures of spectral similarity allow for the recursive generation of a consensus spectrum, which incorporates the most consistent features from statistically similar replicate spectra. Taking the spectral dot product and 95% confidence intervals between consensus spectra from different samples yields the similarity between these samples. Applying the data analysis scheme to replicates of brain tubulin CNBr peptides enables a robust comparison of tubulin isotype expression and post-translational modification patterns in rat and cow brains.
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Affiliation(s)
- Matthew T Olson
- Laboratory of Cellular and Molecular Biophysics, National Institute of Child Health and Human Development, NIH, Bethesda, Maryland 20892, USA
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16
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Abstract
Tubulin, the most abundant axonemal protein, is extensively modified by several highly conserved post-translational mechanisms including acetylation, detyrosination, glutamylation, and glycylation. We discuss the pathways that contribute to the assembly and maintenance of axonemal microtubules, with emphasis on the potential functions of post-translational modifications that affect tubulin. The recent identification of a number of tubulin modifying enzymes and mutational studies of modification sites on tubulin have allowed for significant functional insights. Polymeric modifications of tubulin (glutamylation and glycylation) have emerged as important determinants of the 9 + 2 axoneme assembly and motility.
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Affiliation(s)
- Jacek Gaertig
- Department of Cellular Biology, University of Georgia, Athens, Georgia, USA
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Lakämper S, Meyhöfer E. Back on track – On the role of the microtubule for kinesin motility and cellular function. J Muscle Res Cell Motil 2006; 27:161-71. [PMID: 16453157 DOI: 10.1007/s10974-005-9052-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2005] [Accepted: 12/08/2005] [Indexed: 10/25/2022]
Abstract
The evolution of cytoskeletal filaments (actin- and intermediate-filaments, and the microtubules) and their associated motor- and non-motor-proteins has enabled the eukaryotic cell to achieve complex organizational and structural tasks. This ability to control cellular transport processes and structures allowed for the development of such complex cellular organelles like cilia or flagella in single-cell organisms and made possible the development and differentiation of multi-cellular organisms with highly specialized, polarized cells. Also, the faithful segregation of large amounts of genetic information during cell division relies crucially on the reorganization and control of the cytoskeleton, making the cytoskeleton a key prerequisite for the development of highly complex genomes. Therefore, it is not surprising that the eukaryotic cell continuously invests considerable resources in the establishment, maintenance, modification and rearrangement of the cytoskeletal filaments and the regulation of its interaction with accessory proteins. Here we review the literature on the interaction between microtubules and motor-proteins of the kinesin-family. Our particular interest is the role of the microtubule in the regulation of kinesin motility and cellular function. After an introduction of the kinesin-microtubule interaction we focus on two interrelated aspects: (1) the active allosteric participation of the microtubule during the interaction with kinesins in general and (2) the possible regulatory role of post-translational modifications of the microtubule in the kinesin-microtubule interaction.
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Affiliation(s)
- Stefan Lakämper
- Physics of Complex Systems, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
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