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Protein & Peptide Letters

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ISSN (Print): 0929-8665
ISSN (Online): 1875-5305

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General Research Article

Characterization of an Intermediate Filament Protein from the Platyhelminth, Dugesia japonica

Author(s): Akiko Yamamoto, Ken-ichiro Matsunaga, Toyoaki Anai, Hitoshi Kawano, Toshihisa Ueda, Toshihiko Matsumoto and Shoji Ando*

Volume 27, Issue 5, 2020

Page: [432 - 446] Pages: 15

DOI: 10.2174/0929866526666191025102902

Price: $65

Abstract

Background: Intermediate Filaments (IFs) are major constituents of the cytoskeletal systems in animal cells.

Objective: To gain insights into the structure-function relationship of invertebrate cytoplasmic IF proteins, we characterized an IF protein from the platyhelminth, Dugesia japonica, termed Dif-1.

Methods: cDNA cloning, in situ hybridization, immunohistochemical analysis, and IF assembly experiments in vitro using recombinant Dif-1, were performed for protein characterization.

Results: The structure deduced from the cDNA sequence showed that Djf-1 comprises 568 amino acids and has a tripartite domain structure (N-terminal head, central rod, and C-terminal tail) that is characteristic of IF proteins. Similar to nuclear IF lamins, Djf-1 contains an extra 42 residues in the coil 1b subdomain of the rod domain that is absent from vertebrate cytoplasmic IF proteins and a nuclear lamin-homology segment of approximately 105 residues in the tail domain; however, it contains no nuclear localization signal. In situ hybridization analysis showed that Djf-1 mRNA is specifically expressed in cells located within the marginal region encircling the worm body. Immunohistochemical analysis showed that Djf-1 protein forms cytoplasmic IFs located close to the microvilli of the cells. In vitro IF assembly experiments using recombinant proteins showed that Djf-1 alone polymerizes into IFs. Deletion of the extra 42 residues in the coil 1b subdomain resulted in the failure of IF formation.

Conclusion: Together with data from other histological studies, our results suggest that Djf- 1 is expressed specifically in anchor cells within the glandular adhesive organs of the worm and that Djf-1 IFs may play a role in protecting the cells from mechanical stress.

Keywords: Intermediate filament, molecular evolution, planarian, adhesive organ, structure-function relationship, anchor cells.

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[1]
Fuchs, E.; Weber, K. Intermediate filaments: Structure, dynamics, function, and disease. Annu. Rev. Biochem., 1994, 63, 345-382.
[http://dx.doi.org/10.1146/annurev.bi.63.070194.002021] [PMID: 7979242]
[2]
Parry, D.A.; Steinert, P.M. Intermediate filaments: Molecular architecture, assembly, dynamics and polymorphism. Q. Rev. Biophys., 1999, 32(2), 99-187.
[http://dx.doi.org/10.1017/S0033583500003516] [PMID: 10845237]
[3]
Herrmann, H.; Aebi, U. Intermediate filaments: Molecular structure, assembly mechanism, and integration into functionally distinct intracellular Scaffolds. Annu. Rev. Biochem., 2004, 73, 749-789.
[http://dx.doi.org/10.1146/annurev.biochem.73.011303.073823] [PMID: 15189158]
[4]
Parry, D.A.; Strelkov, S.V.; Burkhard, P.; Aebi, U.; Herrmann, H. Towards a molecular description of intermediate filament structure and assembly. Exp. Cell Res., 2007, 313(10), 2204-2216.
[http://dx.doi.org/10.1016/j.yexcr.2007.04.009] [PMID: 17521629]
[5]
Szeverenyi, I.; Cassidy, A.J.; Chung, C.W.; Lee, B.T.; Common, J.E.; Ogg, S.C.; Chen, H.; Sim, S.Y.; Goh, W.L.; Ng, K.W.; Simpson, J.A.; Chee, L.L.; Eng, G.H.; Li, B.; Lunny, D.P.; Chuon, D.; Venkatesh, A.; Khoo, K.H.; McLean, W.H.; Lim, Y.P.; Lane, E.B. The human intermediate filament database: Comprehensive information on a gene family involved in many human diseases. Hum. Mutat., 2008, 29(3), 351-360.
[http://dx.doi.org/10.1002/humu.20652] [PMID: 18033728]
[6]
Magin, T.M.; Hesse, M.; Meier-Bornheim, R.; Reichelt, J. Developing mouse models to study intermediate filament function. Methods Cell Biol., 2004, 78, 65-94.
[http://dx.doi.org/10.1016/S0091-679X(04)78004-8] [PMID: 15646616]
[7]
Stuurman, N.; Heins, S.; Aebi, U. Nuclear lamins: Their structure, assembly, and interactions. J. Struct. Biol., 1998, 122(1-2), 42-66.
[http://dx.doi.org/10.1006/jsbi.1998.3987] [PMID: 9724605]
[8]
Erber, A.; Riemer, D.; Hofemeister, H.; Bovenschulte, M.; Stick, R.; Panopoulou, G.; Lehrach, H.; Weber, K. Characterization of the Hydra lamin and its gene: A molecular phylogeny of metazoan lamins. J. Mol. Evol., 1999, 49(2), 260-271.
[http://dx.doi.org/10.1007/PL00006548] [PMID: 10441677]
[9]
Goldman, R.D.; Gruenbaum, Y.; Moir, R.D.; Shumaker, D.K.; Spann, T.P. Nuclear lamins: Building blocks of nuclear architecture. Genes Dev., 2002, 16(5), 533-547.
[http://dx.doi.org/10.1101/gad.960502] [PMID: 11877373]
[10]
Erber, A.; Riemer, D.; Bovenschulte, M.; Weber, K. Molecular phylogeny of metazoan intermediate filament proteins. J. Mol. Evol., 1998, 47(6), 751-762.
[http://dx.doi.org/10.1007/PL00006434] [PMID: 9847417]
[11]
Peter, A.; Stick, R. Evolutionary aspects in intermediate filament proteins. Curr. Opin. Cell Biol., 2015, 32, 48-55.
[http://dx.doi.org/10.1016/j.ceb.2014.12.009] [PMID: 25576801]
[12]
Karabinos, A.; Schmidt, H.; Harborth, J.; Schnabel, R.; Weber, K. Essential roles for four cytoplasmic intermediate filament proteins in Caenorhabditis elegans development. Proc. Natl. Acad. Sci. USA, 2001, 98(14), 7863-7868.
[http://dx.doi.org/10.1073/pnas.121169998] [PMID: 11427699]
[13]
Karabinos, A.; Schünemann, J.; Weber, K. Most genes encoding cytoplasmic Intermediate Filament (IF) proteins of the nematode Caenorhabditis elegans are required in late embryogenesis. Eur. J. Cell Biol., 2004, 83(9), 457-468.
[http://dx.doi.org/10.1078/0171-9335-00407] [PMID: 15540462]
[14]
Zimek, A.; Weber, K. The gene for a cytoplasmic intermediate filament (IF) protein of the hemichordate Saccoglossus kowalevskii; definition of the unique features of chordate IF proteins. Gene, 2002, 288(1-2), 187-193.
[http://dx.doi.org/10.1016/S0378-1119(02)00484-5] [PMID: 12034508]
[15]
Karabinos, A.; Zimek, A.; Weber, K. The genome of the early chordate Ciona intestinalis encodes only five cytoplasmic intermediate filament proteins including a single type I and type II keratin and a unique IF-annexin fusion protein. Gene, 2004, 326, 123-129.
[http://dx.doi.org/10.1016/j.gene.2003.10.019] [PMID: 14729270]
[16]
Bartnik, E.; Osborn, M.; Weber, K. Intermediate filaments in muscle and epithelial cells of nematodes. J. Cell Biol., 1986, 102(6), 2033-2041.
[http://dx.doi.org/10.1083/jcb.102.6.2033] [PMID: 3519620]
[17]
Dhe-Paganon, S.; Werner, E.D.; Chi, Y.I.; Shoelson, S.E. Structure of the globular tail of nuclear lamin. J. Biol. Chem., 2002, 277(20), 17381-17384.
[http://dx.doi.org/10.1074/jbc.C200038200] [PMID: 11901143]
[18]
Krimm, I.; Ostlund, C.; Gilquin, B.; Couprie, J.; Hossenlopp, P.; Mornon, J.P.; Bonne, G.; Courvalin, J.C.; Worman, H.J.; Zinn-Justin, S. The Ig-like structure of the C-terminal domain of lamin A/C, mutated in muscular dystrophies, cardiomyopathy, and partial lipodystrophy. Structure, 2002, 10(6), 811-823.
[http://dx.doi.org/10.1016/S0969-2126(02)00777-3] [PMID: 12057196]
[19]
Willmer, P. Invertebrate Relationships; Cambridge University Press: New York, 1994.
[20]
Tazaki, A.; Kato, K.; Orii, H.; Agata, K.; Watanabe, K. The body margin of the planarian Dugesia japonica: Characterization by the expression of an intermediate filament gene. Dev. Genes Evol., 2002, 212(8), 365-373.
[http://dx.doi.org/10.1007/s00427-002-0253-0] [PMID: 12203092]
[21]
Ohama, T.; Kumazaki, T.; Hori, H.; Osawa, S.; Takai, M. Fresh-water planarias and a marine planaria are relatively dissimilar in the 5S rRNA sequences. Nucleic Acids Res., 1983, 11(2), 473-476.
[http://dx.doi.org/10.1093/nar/11.2.473] [PMID: 6828375]
[22]
Chou, P.Y.; Fasman, G.D. Empirical predictions of protein conformation. Annu. Rev. Biochem., 1978, 47, 251-276.
[http://dx.doi.org/10.1146/annurev.bi.47.070178.001343] [PMID: 354496]
[23]
Linding, R.; Jensen, L.J.; Diella, F.; Bork, P.; Gibson, T.J.; Russell, R.B. Protein disorder prediction: Implications for structural proteomics. Structure, 2003, 11(11), 1453-1459.
[http://dx.doi.org/10.1016/j.str.2003.10.002] [PMID: 14604535]
[24]
Merrifield, R.B. Solid-phase peptide synthesis. 3. An improved synthesis of bradykinin. Biochemistry, 1964, 3, 1385-1390.
[http://dx.doi.org/10.1021/bi00897a032] [PMID: 14229685]
[25]
Turner, P.C.; Moyer, R.W. A PCR-based method for manipulation of the vaccinia virus genome that eliminates the need for cloning. Biotechniques, 1992, 13(5), 764-771.
[PMID: 1418979]
[26]
Isobe, K.; Gohara, R.; Ueda, T.; Takasaki, Y.; Ando, S. The last twenty residues in the head domain of mouse lamin A contain important structural elements for formation of head-to-tail polymers in vitro. Biosci. Biotechnol. Biochem., 2007, 71(5), 1252-1259.
[http://dx.doi.org/10.1271/bbb.60674] [PMID: 17485847]
[27]
Bradford, M.M. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal. Biochem., 1976, 72, 248-254.
[http://dx.doi.org/10.1016/0003-2697(76)90527-3] [PMID: 942051]
[28]
Inagaki, M.; Matsuoka, Y.; Tsujimura, K.; Ando, S. Dynamic property of intermediate filaments: Regulation by phosphorylation. BioEssays, 1996, 18, 481-487.
[http://dx.doi.org/10.1002/bies.950180610]
[29]
Sivaramakrishnan, S.; Schneider, J.L.; Sitikov, A.; Goldman, R.D.; Ridge, K.M. Shear stress induced reorganization of the keratin intermediate filament network requires phosphorylation by protein kinase C zeta. Mol. Biol. Cell, 2009, 20(11), 2755-2765.
[http://dx.doi.org/10.1091/mbc.e08-10-1028] [PMID: 19357195]
[30]
Dodemont, H.; Riemer, D.; Ledger, N.; Weber, K. Eight genes and alternative RNA processing pathways generate an unexpectedly large diversity of cytoplasmic intermediate filament proteins in the nematode Caenorhabditis elegans. EMBO J., 1994, 13(11), 2625-2638.
[http://dx.doi.org/10.1002/j.1460-2075.1994.tb06553.x] [PMID: 8013462]
[31]
Dodemont, H.; Riemer, D.; Weber, K. Structure of an invertebrate gene encoding cytoplasmic intermediate filament (IF) proteins: Implications for the origin and the diversification of IF proteins. EMBO J., 1990, 9(12), 4083-4094.
[http://dx.doi.org/10.1002/j.1460-2075.1990.tb07630.x] [PMID: 2249666]
[32]
Gruenbaum, Y.; Landesman, Y.; Drees, B.; Bare, J.W.; Saumweber, H.; Paddy, M.R.; Sedat, J.W.; Smith, D.E.; Benton, B.M.; Fisher, P.A. Drosophila nuclear lamin precursor Dm0 is translated from either of two developmentally regulated mRNA species apparently encoded by a single gene. J. Cell Biol., 1988, 106(3), 585-596.
[http://dx.doi.org/10.1083/jcb.106.3.585] [PMID: 3126192]
[33]
Maeno, H.; Sugimoto, K.; Nakajima, N. Genomic structure of the mouse gene (Lmnb1) encoding nuclear lamin B1. Genomics, 1995, 30(2), 342-346.
[http://dx.doi.org/10.1006/geno.1995.9868] [PMID: 8586436]
[34]
Nozaki, M.; Murata, K.; Morita, T.; Matsushiro, A. Isolation of endo A cDNA from mouse 8-cell stage embryos. Biochem. Biophys. Res. Commun., 1988, 154(3), 890-894.
[http://dx.doi.org/10.1016/0006-291X(88)90223-9] [PMID: 2457370]
[35]
Strausberg, R.L.; Feingold, E.A.; Grouse, L.H.; Derge, J.G.; Klausner, R.D.; Collins, F.S.; Wagner, L.; Shenmen, C.M.; Schuler, G.D.; Altschul, S.F.; Zeeberg, B.; Buetow, K.H.; Schaefer, C.F.; Bhat, N.K.; Hopkins, R.F.; Jordan, H.; Moore, T.; Max, S.I.; Wang, J.; Hsieh, F.; Diatchenko, L.; Marusina, K.; Farmer, A.A.; Rubin, G.M.; Hong, L.; Stapleton, M.; Soares, M.B.; Bonaldo, M.F.; Casavant, T.L.; Scheetz, T.E.; Brownstein, M.J.; Usdin, T.B.; Toshiyuki, S.; Carninci, P.; Prange, C.; Raha, S.S.; Loquellano, N.A.; Peters, G.J.; Abramson, R.D.; Mullahy, S.J.; Bosak, S.A.; McEwan, P.J.; McKernan, K.J.; Malek, J.A.; Gunaratne, P.H.; Richards, S.; Worley, K.C.; Hale, S.; Garcia, A.M.; Gay, L.J.; Hulyk, S.W.; Villalon, D.K.; Muzny, D.M.; Sodergren, E.J.; Lu, X.; Gibbs, R.A.; Fahey, J.; Helton, E.; Ketteman, M.; Madan, A.; Rodrigues, S.; Sanchez, A.; Whiting, M.; Madan, A.; Young, A.C.; Shevchenko, Y.; Bouffard, G.G.; Blakesley, R.W.; Touchman, J.W.; Green, E.D.; Dickson, M.C.; Rodriguez, A.C.; Grimwood, J.; Schmutz, J.; Myers, R.M.; Butterfield, Y.S.; Krzywinski, M.I.; Skalska, U.; Smailus, D.E.; Schnerch, A.; Schein, J.E.; Jones, S.J.; Marra, M.A. Mammalian Gene Collection Program Team. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Proc. Natl. Acad. Sci. USA, 2002, 99(26), 16899-16903.
[http://dx.doi.org/10.1073/pnas.242603899] [PMID: 12477932]
[36]
Tyler, S. Comparative ultrastructure of adhesive systems in the Turbellaria. Zoomorphologie, 1976, 84, 1-76.
[http://dx.doi.org/10.1007/BF02568557]
[37]
Geisler, N.; Schünemann, J.; Weber, K.; Häner, M.; Aebi, U. Assembly and architecture of invertebrate cytoplasmic intermediate filaments reconcile features of vertebrate cytoplasmic and nuclear lamin-type intermediate filaments. J. Mol. Biol., 1998, 282(3), 601-617.
[http://dx.doi.org/10.1006/jmbi.1998.1995] [PMID: 9737925]
[38]
Heitlinger, E.; Peter, M.; Lustig, A.; Villiger, W.; Nigg, E.A.; Aebi, U. The role of the head and tail domain in lamin structure and assembly: Analysis of bacterially expressed chicken lamin A and truncated B2 lamins. J. Struct. Biol., 1992, 108(1), 74-89.
[http://dx.doi.org/10.1016/1047-8477(92)90009-Y] [PMID: 1562436]
[39]
Weber, K.; Plessmann, U.; Ulrich, W. Cytoplasmic intermediate filament proteins of invertebrates are closer to nuclear lamins than are vertebrate intermediate filament proteins; sequence characterization of two muscle proteins of a nematode. EMBO J., 1989, 8(11), 3221-3227.
[http://dx.doi.org/10.1002/j.1460-2075.1989.tb08481.x] [PMID: 2583097]
[40]
Karabinos, A.; Schulze, E.; Schünemann, J.; Parry, D.A.; Weber, K. In vivo and in vitro evidence that the four essential intermediate filament (IF) proteins A1, A2, A3 and B1 of the nematode Caenorhabditis elegans form an obligate heteropolymeric IF system. J. Mol. Biol., 2003, 333(2), 307-319.
[http://dx.doi.org/10.1016/j.jmb.2003.08.041] [PMID: 14529618]
[41]
Mical, T.I.; Monteiro, M.J. The role of sequences unique to nuclear intermediate filaments in the targeting and assembly of human lamin B: Evidence for lack of interaction of lamin B with its putative receptor. J. Cell Sci., 1998, 111(Pt 23), 3471-3485.
[PMID: 9811562]
[42]
Mical, T.I.; Luther, P.W.; Monteiro, M.J. Intracellular assembly and sorting of intermediate filament proteins: Role of the 42 amino acid lamin insert. Exp. Cell Res., 2004, 295(1), 183-193.
[http://dx.doi.org/10.1016/j.yexcr.2004.01.006] [PMID: 15051501]
[43]
Monteiro, M.J.; Hicks, C.; Gu, L.; Janicki, S. Determinants for intracellular sorting of cytoplasmic and nuclear intermediate filaments. J. Cell Biol., 1994, 127(5), 1327-1343.
[http://dx.doi.org/10.1083/jcb.127.5.1327] [PMID: 7962093]
[44]
Herrmann, H.; Häner, M.; Brettel, M.; Müller, S.A.; Goldie, K.N.; Fedtke, B.; Lustig, A.; Franke, W.W.; Aebi, U. Structure and assembly properties of the intermediate filament protein vimentin: The role of its head, rod and tail domains. J. Mol. Biol., 1996, 264(5), 933-953.
[http://dx.doi.org/10.1006/jmbi.1996.0688] [PMID: 9000622]
[45]
Coulombe, P.A.; Chan, Y.M.; Albers, K.; Fuchs, E. Deletions in epidermal keratins leading to alterations in filament organization in vivo and in intermediate filament assembly in vitro. J. Cell Biol., 1990, 111(6 Pt 2), 3049-3064.
[http://dx.doi.org/10.1083/jcb.111.6.3049] [PMID: 1702787]
[46]
Raats, J.M.; Pieper, F.R.; Vree Egberts, W.T.; Verrijp, K.N.; Ramaekers, F.C.; Bloemendal, H. Assembly of amino-terminally deleted desmin in vimentin-free cells. J. Cell Biol., 1990, 111(5 Pt 1), 1971-1985.
[http://dx.doi.org/10.1083/jcb.111.5.1971] [PMID: 1699950]
[47]
Wilson, A.K.; Coulombe, P.A.; Fuchs, E. The roles of K5 and K14 head, tail, and R/K L L E G E domains in keratin filament assembly in vitro. J. Cell Biol., 1992, 119(2), 401-414.
[http://dx.doi.org/10.1083/jcb.119.2.401] [PMID: 1383231]
[48]
Traub, P.; Scherbarth, A.; Wiegers, W.; Shoeman, R.L. Salt-stable interaction of the amino-terminal head region of vimentin with the alpha-helical rod domain of cytoplasmic intermediate filament proteins and its relevance to protofilament structure and filament formation and stability. J. Cell Sci., 1992, 101(Pt 2), 363-381.
[PMID: 1629250]
[49]
Gohara, R.; Tang, D.; Inada, H.; Inagaki, M.; Takasaki, Y.; Ando, S. Phosphorylation of vimentin head domain inhibits interaction with the carboxyl-terminal end of alpha-helical rod domain studied by surface plasmon resonance measurements. FEBS Lett., 2001, 489(2-3), 182-186.
[http://dx.doi.org/10.1016/S0014-5793(01)02108-1] [PMID: 11165246]
[50]
Aziz, A.; Hess, J.F.; Budamagunta, M.S.; FitzGerald, P.G.; Voss, J.C. Head and rod 1 interactions in vimentin: Identification of contact sites, structure, and changes with phosphorylation using site-directed spin labeling and electron paramagnetic resonance. J. Biol. Chem., 2009, 284(11), 7330-7338.
[http://dx.doi.org/10.1074/jbc.M809029200] [PMID: 19117942]
[51]
Wang, H.; Parry, D.A.; Jones, L.N.; Idler, W.W.; Marekov, L.N.; Steinert, P.M. In vitro assembly and structure of trichocyte keratin intermediate filaments: A novel role for stabilization by disulfide bonding. J. Cell Biol., 2000, 151(7), 1459-1468.
[http://dx.doi.org/10.1083/jcb.151.7.1459] [PMID: 11134075]
[52]
Parry, D.A.; Marekov, L.N.; Steinert, P.M.; Smith, T.A. A role for the 1A and L1 rod domain segments in head domain organization and function of intermediate filaments: Structural analysis of trichocyte keratin. J. Struct. Biol., 2002, 137(1-2), 97-108.
[http://dx.doi.org/10.1006/jsbi.2002.4437] [PMID: 12064937]
[53]
Hatzfeld, M.; Weber, K. Tailless keratins assemble into regular intermediate filaments in vitro. J. Cell Sci., 1990, 97(Pt 2), 317-324.
[PMID: 1703550]
[54]
Kouklis, P.D.; Papamarcaki, T.; Merdes, A.; Georgatos, S.D. A potential role for the COOH-terminal domain in the lateral packing of type III intermediate filaments. J. Cell Biol., 1991, 114(4), 773-786.
[http://dx.doi.org/10.1083/jcb.114.4.773] [PMID: 1714461]
[55]
Bousquet, O.; Ma, L.; Yamada, S.; Gu, C.; Idei, T.; Takahashi, K.; Wirtz, D.; Coulombe, P.A. The nonhelical tail domain of keratin 14 promotes filament bundling and enhances the mechanical properties of keratin intermediate filaments in vitro. J. Cell Biol., 2001, 155(5), 747-754.
[http://dx.doi.org/10.1083/jcb.200104063] [PMID: 11724817]

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