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Fujita Y, Chokki T, Nishioka T, Morimoto K, Nakayama A, Nakae H, Ogasawara M, Terasaki AG. The emergence of nebulin repeats and evolution of lasp family proteins. Cytoskeleton (Hoboken) 2022; 78:419-435. [PMID: 35224880 DOI: 10.1002/cm.21693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 02/23/2022] [Accepted: 02/25/2022] [Indexed: 11/10/2022]
Abstract
The LIM and SH3 domain protein (lasp) family, the smallest proteins in the nebulin superfamily, consists of vertebrate lasp-1 expressed in various non-muscle tissues, vertebrate lasp-2 expressed in the brain and cardiac muscle, and invertebrate lasp whose functions have been analyzed in Ascidiacea and Insecta. Gene evolution of the lasp family proteins was investigated by multiple alignments, comparison of gene structure, and synteny analyses in eukaryotes in which mRNA expression was confirmed. All invertebrates analyzed in this study belonging to the clade Filasterea, with the exception of Placozoa, have at least one lasp gene. The minimal actin-binding region (LIM domain and first nebulin repeat) and SH3 domain detected in vertebrate lasp-2 were found to be conserved among the lasp family proteins, and we showed that nematode lasp has actin-binding activity. The linker sequences vary among invertebrate lasp proteins, implying that the lasp family proteins have universal and diverse functions. Gene structures and syntenic analyses suggest that a gene fragment encoding two nebulin repeats and a linker emerged in Filasterea or Holozoa, and the first lasp gene was generated following combination of three gene fragments encoding the LIM domain, two nebulin repeats with a linker, and the SH3 domain. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Yuki Fujita
- Department of Biology, Graduate School of Science, Chiba University, Yayoi-cho, Inage-ku, Chiba, Japan
| | - Tamami Chokki
- Department of Biology, Graduate School of Science, Chiba University, Yayoi-cho, Inage-ku, Chiba, Japan
| | - Tatsuji Nishioka
- Department of Biology, Graduate School of Science, Chiba University, Yayoi-cho, Inage-ku, Chiba, Japan
| | - Kouta Morimoto
- Department of Biology, Graduate School of Science, Chiba University, Yayoi-cho, Inage-ku, Chiba, Japan
| | - Ayako Nakayama
- Department of Biology, Graduate School of Science, Chiba University, Yayoi-cho, Inage-ku, Chiba, Japan
| | - Hiroki Nakae
- BIO-Business Solutions, Hisamoto, Takatsu-ku, Kawasaki, Japan
| | - Michio Ogasawara
- Department of Biology, Graduate School of Science, Chiba University, Yayoi-cho, Inage-ku, Chiba, Japan
| | - Asako G Terasaki
- Department of Biology, Graduate School of Science, Chiba University, Yayoi-cho, Inage-ku, Chiba, Japan
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Nishikawa A, Hanashima A, Nakayama S, Ogasawara M, Kimura S. Transcripts of the nebulin gene from Ciona heart and their implications for the evolution of nebulin family genes. Gene X 2019; 716:144036. [DOI: 10.1016/j.gene.2019.144036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 07/27/2019] [Accepted: 07/31/2019] [Indexed: 10/26/2022] Open
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Hanashima A, Kawamura Y, Nakauchi Y. A great legacy of muscle research and education from Dr. Sumiko Kimura. Cytoskeleton (Hoboken) 2019; 76:298-302. [PMID: 31152497 DOI: 10.1002/cm.21542] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 05/16/2019] [Accepted: 05/28/2019] [Indexed: 11/07/2022]
Abstract
Dr. Sumiko Kimura, a former professor of biology at Chiba University, was known as a distinguished biochemist who contributed considerably to our knowledge about the cytoskeleton of muscle cells, especially through her work on connectin (also called titin) and actin regulatory proteins. Sadly, she suddenly passed away in Tokyo on November 1, 2018 at the age of 71. She succumbed to multiple organ failure caused by a bacterial infection following a third operation on her heart. Dr. Kimura had been continuing her research into connectin right up until several months before her decease.
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Affiliation(s)
- Akira Hanashima
- First Department of Physiology, Kawasaki Medical School, Kurashiki, Japan
| | - Yuuki Kawamura
- Faculty of Medicine, Department of Liberal Arts (Biology), Saitama Medical University, Moroyama, Japan
| | - Yuni Nakauchi
- Faculty of Science, Department of Science (Biology), Yamagata University, Yamagata, Japan
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Hanashima A. Obituary: Sumiko Kimura 1947–2018. J Muscle Res Cell Motil 2018; 39:149-51. [DOI: 10.1007/s10974-019-09506-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Peterson MP, Whittaker DJ, Ambreth S, Sureshchandra S, Buechlein A, Podicheti R, Choi JH, Lai Z, Mockatis K, Colbourne J, Tang H, Ketterson ED. De novo transcriptome sequencing in a songbird, the dark-eyed junco (Junco hyemalis): genomic tools for an ecological model system. BMC Genomics 2012; 13:305. [PMID: 22776250 PMCID: PMC3476391 DOI: 10.1186/1471-2164-13-305] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2011] [Accepted: 07/09/2012] [Indexed: 11/25/2022] Open
Abstract
Background Though genomic-level data are becoming widely available, many of the metazoan species sequenced are laboratory systems whose natural history is not well documented. In contrast, the wide array of species with very well-characterized natural history have, until recently, lacked genomics tools. It is now possible to address significant evolutionary genomics questions by applying high-throughput sequencing to discover the majority of genes for ecologically tractable species, and by subsequently developing microarray platforms from which to investigate gene regulatory networks that function in natural systems. We used GS-FLX Titanium Sequencing (Roche/454-Sequencing) of two normalized libraries of pooled RNA samples to characterize a transcriptome of the dark-eyed junco (Junco hyemalis), a North American sparrow that is a classically studied species in the fields of photoperiodism, speciation, and hormone-mediated behavior. Results From a broad pool of RNA sampled from tissues throughout the body of a male and a female junco, we sequenced a total of 434 million nucleotides from 1.17 million reads that were assembled de novo into 31,379 putative transcripts representing 22,765 gene sets covering 35.8 million nucleotides with 12-fold average depth of coverage. Annotation of roughly half of the putative genes was accomplished using sequence similarity, and expression was confirmed for the majority with a preliminary microarray analysis. Of 716 core bilaterian genes, 646 (90 %) were recovered within our characterized gene set. Gene Ontology, orthoDB orthology groups, and KEGG Pathway annotation provide further functional information about the sequences, and 25,781 potential SNPs were identified. Conclusions The extensive sequence information returned by this effort adds to the growing store of genomic data on diverse species. The extent of coverage and annotation achieved and confirmation of expression, show that transcriptome sequencing provides useful information for ecological model systems that have historically lacked genomic tools. The junco-specific microarray developed here is allowing investigations of gene expression responses to environmental and hormonal manipulations – extending the historic work on natural history and hormone-mediated phenotypes in this system.
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Affiliation(s)
- Mark P Peterson
- Dept. of Biology, Center for Integrated Study of Animal Behavior, Indiana University, Bloomington, IN, USA.
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Ohtsuka S, Hanashima A, Kubokawa K, Bao Y, Tando Y, Kohmaru J, Nakaya H, Maruyama K, Kimura S. Amphioxus connectin exhibits merged structure as invertebrate connectin in I-band region and vertebrate connectin in A-band region. J Mol Biol 2011; 409:415-26. [PMID: 21510959 DOI: 10.1016/j.jmb.2011.04.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2010] [Revised: 03/10/2011] [Accepted: 04/05/2011] [Indexed: 11/16/2022]
Abstract
Connectin is an elastic protein found in vertebrate striated muscle and in some invertebrates as connectin-like proteins. In this study, we determined the structure of the amphioxus connectin gene and analyzed its sequence based on its genomic information. Amphioxus is not a vertebrate but, phylogenetically, the lowest chordate. Analysis of gene structure revealed that the amphioxus gene is approximately 430 kb in length and consists of regions with exons of repeatedly aligned immunoglobulin (Ig) domains and regions with exons of fibronectin type 3 and Ig domain repeats. With regard to this sequence, although the region corresponding to the I-band is homologous to that of invertebrate connectin-like proteins and has an Ig-PEVK region similar to that of the Neanthes sp. 4000K protein, the region corresponding to the A-band has a super-repeat structure of Ig and fibronectin type 3 domains and a kinase domain near the C-terminus, which is similar to the structure of vertebrate connectin. These findings revealed that amphioxus connectin has the domain structure of invertebrate connectin-like proteins at its N-terminus and that of vertebrate connectin at its C-terminus. Thus, amphioxus connectin has a novel structure among known connectin-like proteins. This finding suggests that the formation and maintenance of the sarcomeric structure of amphioxus striated muscle are similar to those of vertebrates; however, its elasticity is different from that of vertebrates, being more similar to that of invertebrates.
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Affiliation(s)
- Satoshi Ohtsuka
- Department of Biology, Graduate School of Science, Chiba University, Japan
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Abstract
Nebulin is a giant 600- to 900-kDa filamentous protein that is an integral component of the skeletal muscle thin filament. Its functions have remained largely nebulous because of its large size and the difficulty in extracting nebulin in a native state from muscle. Recent improvements in the field, especially the development of knockout mouse models deficient in nebulin (NEB-KO mice), indicate now that nebulin performs a surprisingly wide range of functions. In addition to a major role in thin-filament length specification, nebulin also functions in the regulation of muscle contraction, as indicated by the findings that muscle fibers deficient in nebulin have a higher tension cost, and develop less force due to reduced myofilament calcium sensitivity and altered crossbridge cycling kinetics. In addition, the function of nebulin extends to a role in calcium homeostasis. These novel functions indicate that nebulin might have evolved in vertebrate skeletal muscles to develop high levels of muscle force efficiently. Finally, the NEB-KO mouse models also highlight the role of nebulin in the assembly and alignment of the Z disks. Notably, rapid progress in understanding the roles of nebulin in vivo provides clinically important insights into how nebulin deficiency in patients with nemaline myopathy contributes to debilitating muscle weakness.
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Affiliation(s)
- Siegfried Labeit
- Department of Integrative Pathophysiology, Universitätsmedizin Mannheim, University of Heidelberg, Mannheim, Germany.
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Björklund ÅK, Light S, Sagit R, Elofsson A. Nebulin: A Study of Protein Repeat Evolution. J Mol Biol 2010; 402:38-51. [DOI: 10.1016/j.jmb.2010.07.011] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2010] [Revised: 06/22/2010] [Accepted: 07/07/2010] [Indexed: 11/22/2022]
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Chitose R, Watanabe A, Asano M, Hanashima A, Sasano K, Bao Y, Maruyama K, Kimura S. Isolation of nebulin from rabbit skeletal muscle and its interaction with actin. J Biomed Biotechnol 2010; 2010:108495. [PMID: 20467585 DOI: 10.1155/2010/108495] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2009] [Accepted: 02/15/2010] [Indexed: 12/11/2022] Open
Abstract
Nebulin is about 800 kDa filamentous protein that binds the entire thin filament of vertebrate skeletal muscle sarcomeres. Nebulin cannot be isolated from muscle except in a completely denatured form by direct solubilization of myofibrils with SDS because nebulin is hardly soluble under salt conditions. In the present study, nebulin was solubilized by a salt solution containing 1 M urea and purified by DEAE-Toyopearl column chromatography via 4 M urea elution. Rotary-shadowed images of nebulin showed entangled knit-like particles, about 20 nm in diameter. The purified nebulin bound to actin filaments to form loose bundles. Nebulin was confirmed to bind actin, α-actinin, β-actinin, and tropomodulin, but not troponin or tropomyosin. The data shows that full-length nebulin can be also obtained in a functional and presumably native form, verified by data from experiments using recombinant subfragments.
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Hanashima A, Kubokawa K, Kimura S. Structure of the amphioxus nebulin gene and evolution of the nebulin family genes. Gene 2009; 443:76-82. [PMID: 19406219 DOI: 10.1016/j.gene.2009.04.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2009] [Revised: 04/16/2009] [Accepted: 04/21/2009] [Indexed: 11/21/2022]
Abstract
Nebulin family genes are believed to have diverged from a single gene during the evolution of vertebrates. We determined the structure of the amphioxus nebulin gene and showed that in addition to the features of the human nebulin gene, this gene had a LIM domain, secondary super repeats and a giant exon with 98 nebulin repeats containing unique sequences. A transcript of this gene amplified by reverse transcriptase-polymerase chain reaction had a LIM domain, three nebulin repeats and an SH3 domain. This transcript was similar to an isoform of human nebulette (Lasp-2). Phylogenetic analysis using the LIM and SH3 domains of the nebulin family proteins showed that amphioxus nebulin is located outside the vertebrate nebulin family group in the phylogenetic tree. These results indicated that the amphioxus nebulin gene had a unified structure among nebulin, nebulette, lasp-1 and N-RAP of vertebrates, and that these nebulin family genes diverged from the amphioxus nebulin gene during the course of vertebrate evolution.
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