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Kimura Y, Nikaido M. Unveiling the expansion of keratin genes in lungfishes: a possible link to terrestrial adaptation. Genes Genet Syst 2023; 98:249-257. [PMID: 37853642 DOI: 10.1266/ggs.23-00188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2023] Open
Abstract
Keratins are intermediate filament proteins that are important for epidermal strength and protection from desiccation. Keratin genes are highly duplicated and have diversified by forming two major clusters in the genomes of terrestrial vertebrates. The keratin genes of lungfishes, the closest fish to tetrapods, have not been studied at the genomic level, despite the importance of lungfishes in terrestrial adaptation. Here, we identified keratin genes in the genomes of two lungfish species and performed syntenic and phylogenetic analyses. Additionally, we identified keratin genes from two gobies and two mudskippers, inhabiting underwater and terrestrial environments. We found that in lungfishes, keratin genes were duplicated and diversified within two major clusters, similar to but independent of terrestrial vertebrates. By contrast, keratin genes were not notably duplicated in mudskippers. The results indicate that keratin gene duplication occurred repeatedly in lineages close to tetrapods, but not in teleost fish, even in species adapted to terrestrial environments.
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Affiliation(s)
- Yuki Kimura
- School of Life Science and Technology, Tokyo Institute of Technology
| | - Masato Nikaido
- School of Life Science and Technology, Tokyo Institute of Technology
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2
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Xia L, Li C, Zhao Y, Zhang W, Hu C, Qu Y, Li H, Yan J, Zhou K, Li P. Expression analysis of alpha keratins and corneous beta-protein genes during embryonic development of Gekko japonicus. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2023; 47:101116. [PMID: 37567027 DOI: 10.1016/j.cbd.2023.101116] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 08/01/2023] [Accepted: 08/02/2023] [Indexed: 08/13/2023]
Abstract
Epidermal appendages of birds and reptiles, including claws, feathers, scales, and setae, are primarily composed of alpha keratins (KRTs) and corneous beta-proteins (CBPs). A comprehensive and systematic knowledge of KRTs and CBPs in Schlegel's Japanese gecko (Gekko japonicus) is still lacking. In this study, 22 candidate Gecko japonicus keratin (GjKRT) family genes (12 type I genes, 10 type II genes) were identified in the G. japonicus genome. The majority of GjKRT genes across various subgroups had undergone a prolonged and highly conservative evolutionary process. Through a combination of morphological observation, RNA-seq analysis, and qRT-PCR assay, it was possible to discern the dynamic alterations in the expression of GjKRTs and Gecko japonicus corneous beta-proteins genes (GjCBPs). These findings strongly indicate that GjKRTs gradually accumulate to constitute an α-layer, which is subsequently succeeded by the formation of the corneous beta layer containing GjCBPs at late stages (40-42) of embryonic development. The epidermal appendages in G. japonicus may result from the joint accumulation of KRTs and CBPs, with stages 40-42 being critical for their development. These findings provide novel insights into KRTs and CBPs of G. japonicus and offer a foundation for investigating the functions of GjKRT and GjCBP gene families. Furthermore, this knowledge contributes to unraveling the molecular mechanisms underlying the formation of epidermal appendages in G. japonicus.
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Affiliation(s)
- Longjie Xia
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, Jiangsu, PR China
| | - Chao Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, Jiangsu, PR China
| | - Yue Zhao
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, Jiangsu, PR China
| | - Wenyi Zhang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, Jiangsu, PR China
| | - Chaochao Hu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, Jiangsu, PR China
| | - Yanfu Qu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, Jiangsu, PR China
| | - Hong Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, Jiangsu, PR China
| | - Jie Yan
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, Jiangsu, PR China
| | - Kaiya Zhou
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, Jiangsu, PR China
| | - Peng Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, Jiangsu, PR China.
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Ho M, Thompson B, Fisk JN, Nebert DW, Bruford EA, Vasiliou V, Bunick CG. Update of the keratin gene family: evolution, tissue-specific expression patterns, and relevance to clinical disorders. Hum Genomics 2022; 16:1. [PMID: 34991727 PMCID: PMC8733776 DOI: 10.1186/s40246-021-00374-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 12/17/2021] [Indexed: 12/15/2022] Open
Abstract
Intermediate filament (IntFil) genes arose during early metazoan evolution, to provide mechanical support for plasma membranes contacting/interacting with other cells and the extracellular matrix. Keratin genes comprise the largest subset of IntFil genes. Whereas the first keratin gene appeared in sponge, and three genes in arthropods, more rapid increases in keratin genes occurred in lungfish and amphibian genomes, concomitant with land animal-sea animal divergence (~ 440 to 410 million years ago). Human, mouse and zebrafish genomes contain 18, 17 and 24 non-keratin IntFil genes, respectively. Human has 27 of 28 type I "acidic" keratin genes clustered at chromosome (Chr) 17q21.2, and all 26 type II "basic" keratin genes clustered at Chr 12q13.13. Mouse has 27 of 28 type I keratin genes clustered on Chr 11, and all 26 type II clustered on Chr 15. Zebrafish has 18 type I keratin genes scattered on five chromosomes, and 3 type II keratin genes on two chromosomes. Types I and II keratin clusters-reflecting evolutionary blooms of keratin genes along one chromosomal segment-are found in all land animal genomes examined, but not fishes; such rapid gene expansions likely reflect sudden requirements for many novel paralogous proteins having divergent functions to enhance species survival following sea-to-land transition. Using data from the Genotype-Tissue Expression (GTEx) project, tissue-specific keratin expression throughout the human body was reconstructed. Clustering of gene expression patterns revealed similarities in tissue-specific expression patterns for previously described "keratin pairs" (i.e., KRT1/KRT10, KRT8/KRT18, KRT5/KRT14, KRT6/KRT16 and KRT6/KRT17 proteins). The ClinVar database currently lists 26 human disease-causing variants within the various domains of keratin proteins.
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Affiliation(s)
- Minh Ho
- Department of Dermatology, Yale University, 333 Cedar St., LCI 501, PO Box 208059, New Haven, CT, 06520-8059, USA
| | - Brian Thompson
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, CT, 06511, USA
| | - Jeffrey Nicholas Fisk
- Program of Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06511, USA
| | - Daniel W Nebert
- Departments of Pediatrics and Molecular and Developmental Biology, Cincinnati Children's Research Center, Cincinnati, OH, 45229, USA
- Department of Environmental Health and Center for Environmental Genetics, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - Elspeth A Bruford
- HUGO Gene Nomenclature Committee (HGNC), EMBL-EBI, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
- Department of Haematology, University of Cambridge, Cambridge, CB2 0XY, UK
| | - Vasilis Vasiliou
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, CT, 06511, USA
| | - Christopher G Bunick
- Department of Dermatology, Yale University, 333 Cedar St., LCI 501, PO Box 208059, New Haven, CT, 06520-8059, USA.
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA.
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Parry DAD, Winter DJ. Keratin intermediate filament chains in the European common wall lizard (Podarcis muralis) and a potential keratin filament crosslinker. J Struct Biol 2021; 213:107793. [PMID: 34481988 DOI: 10.1016/j.jsb.2021.107793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 08/10/2021] [Accepted: 08/29/2021] [Indexed: 10/20/2022]
Abstract
On the basis of sequence homology with mammalian α-keratins, and on the criteria that the coiled-coil segments and central linker in the rod domain of these molecules must have conserved lengths if they are to assemble into viable intermediate filaments, a total of 28 Type I and Type II keratin intermediate filament chains (KIF) have been identified from the genome of the European common wall lizard (Podarcis muralis). Using the same criteria this number may be compared to 33 found here in the green anole lizard (Anole carolinensis) and 25 in the tuatara (Sphenodon punctatus). The Type I and Type II KIF genes in the wall lizard fall in clusters on chromosomes 13 and 2 respectively. Although some differences occur in the terminal domains in the KIF chains of the two lizards and tuatara, the similarities between key indicator residues - cysteine, glycine and proline - are significant. The terminal domains of the KIF chains in the wall lizard also contain sequence repeats commonly based on glycine and large apolar residues and would permit the fine tuning of physical properties when incorporated within the intermediate filaments. The H1 domain in the Type II chain is conserved across the lizards, tuatara and mammals, and has been related to its role in assembly at the 2-4 molecule level. A KIF-like chain (K80) with an extensive tail domain comprised of multiple tandem repeats has been identified as having a potential filament-crosslinking role.
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Affiliation(s)
- David A D Parry
- School of Fundamental Sciences, Massey University, Private Bag 11-222, Palmerston North 4442, New Zealand.
| | - David J Winter
- School of Fundamental Sciences, Massey University, Private Bag 11-222, Palmerston North 4442, New Zealand
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Parry DAD, Winter DJ. Keratin intermediate filament chains in tuatara (Sphenodon punctatus): A comparison of tuatara and human sequences. J Struct Biol 2021; 213:107706. [PMID: 33577903 DOI: 10.1016/j.jsb.2021.107706] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 01/27/2021] [Accepted: 01/28/2021] [Indexed: 11/19/2022]
Abstract
Determination of the sequences of the keratin intermediate filament chains in tuatara has shown that these are closely akin to the α-keratins in human and other vertebrates, especially in the central, coiled-coil rod region. The domain lengths within the rod are preserved exactly, both Type I and Type II chains have been recognised, and sequence identity/homology exists between their respective chains. Nonetheless, there are characteristic differences in amino acid composition and sequence between their respective head (N-terminal) domains and their tail (C-terminal) domains, though some similarities are retained. Further, there is evidence of tandem repeats of a variety of lengths in the tuatara heads and tails indicative of sequence duplication events. These are not evident in human α-keratins and would therefore have implications for the physical attributes of the tissues in the two species. Multiple families of keratin-associated proteins that are ultra-high cysteine-rich or glycine + tyrosine-rich in human and other species do not have direct equivalents in the tuatara. Although high-sulphur proteins are present in tuatara the cysteine residue contents are significantly lower than in human. Further, no sequence homologies between the HS proteins in the two species have been found, thereby casting considerable doubt as to whether any matrix-forming high-sulphur proteins exist in tuatara. These observations may be correlated with the numerous cysteine-rich β-keratins (corneous β-proteins) that are present in tuatara, but which are conspicuously absent in mammals.
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Affiliation(s)
- David A D Parry
- School of Fundamental Sciences, Massey University, Private Bag 11-222, Palmerston North 4442, New Zealand.
| | - David J Winter
- School of Fundamental Sciences, Massey University, Private Bag 11-222, Palmerston North 4442, New Zealand
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Kimura Y, Nikaido M. Conserved keratin gene clusters in ancient fish: An evolutionary seed for terrestrial adaptation. Genomics 2020; 113:1120-1128. [PMID: 33189779 DOI: 10.1016/j.ygeno.2020.11.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 10/05/2020] [Accepted: 11/09/2020] [Indexed: 11/26/2022]
Abstract
Type I and type II keratins are subgroups of intermediate filament proteins that provide toughness to the epidermis and protect it from water loss. In terrestrial vertebrates, the keratin genes form two major clusters, clusters 1 and 2, each of which is dominated by type I and II keratin genes. By contrast, such clusters are not observed in teleost fish. Although the diversification of keratins is believed to have made a substantial contribution to terrestrial adaptation, its evolutionary process has not been clarified. Here, we performed a comprehensive genomic survey of the keratin genes of a broad range of vertebrates. As a result, we found that ancient fish lineages such as elephant shark, reedfish, spotted gar, and coelacanth share both keratin gene clusters. We also discovered an expansion of keratin genes that form a novel subcluster in reedfish. Syntenic and phylogenetic analyses revealed that two pairs of krt18/krt8 keratin genes were shared among all vertebrates, thus implying that they encode ancestral type I and II keratin protein sets. We further revealed that distinct keratin gene subclusters, which show specific expressions in the epidermis of adult amphibians, stemmed from canonical keratin genes in non-terrestrial ancestors. Molecular evolutionary analyses suggested that the selective constraints were relaxed in the adult epidermal subclusters of amphibians as well as the novel subcluster of reedfish. The results of the present study represent the process of diversification of keratins through a series of gene duplications that could have facilitated the terrestrial adaptation of vertebrates.
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Affiliation(s)
- Yuki Kimura
- School of Life Science and Technology, Tokyo Institute of Technology, Japan
| | - Masato Nikaido
- School of Life Science and Technology, Tokyo Institute of Technology, Japan.
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7
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Siomava N, Fuentes JSM, Diogo R. Deconstructing the long‐standing a priori assumption that serial homology generally involves ancestral similarity followed by anatomical divergence. J Morphol 2020; 281:1110-1132. [DOI: 10.1002/jmor.21236] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 06/18/2020] [Accepted: 07/07/2020] [Indexed: 12/26/2022]
Affiliation(s)
- Natalia Siomava
- Department of Anatomy Howard University College of Medicine Washington District of Columbia USA
| | | | - Rui Diogo
- Department of Anatomy Howard University College of Medicine Washington District of Columbia USA
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Shen Y, He Y, Bi Y, Chen J, Zhao Z, Li J, Chen X. Transcriptome analysis of gill from Lateolabrax maculatus and aqp3 gene expression. AQUACULTURE AND FISHERIES 2019. [DOI: 10.1016/j.aaf.2019.03.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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9
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Ehrlich F, Fischer H, Langbein L, Praetzel-Wunder S, Ebner B, Figlak K, Weissenbacher A, Sipos W, Tschachler E, Eckhart L. Differential Evolution of the Epidermal Keratin Cytoskeleton in Terrestrial and Aquatic Mammals. Mol Biol Evol 2019; 36:328-340. [PMID: 30517738 PMCID: PMC6367960 DOI: 10.1093/molbev/msy214] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Keratins are the main intermediate filament proteins of epithelial cells. In keratinocytes of the mammalian epidermis they form a cytoskeleton that resists mechanical stress and thereby are essential for the function of the skin as a barrier against the environment. Here, we performed a comparative genomics study of epidermal keratin genes in terrestrial and fully aquatic mammals to determine adaptations of the epidermal keratin cytoskeleton to different environments. We show that keratins K5 and K14 of the innermost (basal), proliferation-competent layer of the epidermis are conserved in all mammals investigated. In contrast, K1 and K10, which form the main part of the cytoskeleton in the outer (suprabasal) layers of the epidermis of terrestrial mammals, have been lost in whales and dolphins (cetaceans) and in the manatee. Whereas in terrestrial mammalian epidermis K6 and K17 are expressed only upon stress-induced epidermal thickening, high levels of K6 and K17 are consistently present in dolphin skin, indicating constitutive expression and substitution of K1 and K10. K2 and K9, which are expressed in a body site-restricted manner in human and mouse suprabasal epidermis, have been lost not only in cetaceans and manatee but also in some terrestrial mammals. The evolution of alternative splicing of K10 and differentiation-dependent upregulation of K23 have increased the complexity of keratin expression in the epidermis of terrestrial mammals. Taken together, these results reveal evolutionary diversification of the epidermal cytoskeleton in mammals and suggest a complete replacement of the quantitatively predominant epidermal proteins of terrestrial mammals by originally stress-inducible keratins in cetaceans.
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Affiliation(s)
- Florian Ehrlich
- Research Division of Biology and Pathobiology of the Skin, Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Heinz Fischer
- Research Division of Biology and Pathobiology of the Skin, Department of Dermatology, Medical University of Vienna, Vienna, Austria.,Division of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
| | - Lutz Langbein
- Department of Genetics of Skin Carcinogenesis, German Cancer Research Center, Heidelberg, Germany
| | - Silke Praetzel-Wunder
- Department of Genetics of Skin Carcinogenesis, German Cancer Research Center, Heidelberg, Germany
| | - Bettina Ebner
- Research Division of Biology and Pathobiology of the Skin, Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Katarzyna Figlak
- Research Division of Biology and Pathobiology of the Skin, Department of Dermatology, Medical University of Vienna, Vienna, Austria.,Centre for Cell Biology and Cutaneous Research, Blizard Institute, Queen Mary University of London, London, United Kingdom
| | | | - Wolfgang Sipos
- Clinical Department for Farm Animals and Herd Management, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Erwin Tschachler
- Research Division of Biology and Pathobiology of the Skin, Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Leopold Eckhart
- Research Division of Biology and Pathobiology of the Skin, Department of Dermatology, Medical University of Vienna, Vienna, Austria
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Keratinization and mucogenesis in the epidermis of an angler catfish Chaca chaca (Siluriformes, Chacidae): A Histochemical and fluorescence microscope investigation. ZOOLOGY 2018; 131:10-19. [PMID: 30502823 DOI: 10.1016/j.zool.2018.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 10/09/2018] [Accepted: 10/09/2018] [Indexed: 11/21/2022]
Abstract
The present study describes keratinization and mucogenesis in the epidermis of an angler catfish Chaca chaca, using a series of immunochemical, fluorescence and histochemical methods. The epidermis is primarily mucogenic and shows characteristic specialised structures at irregular intervals. These structures are identified keratinized in nature. The superficial layer epithelial cells in the keratinized structures often detach from the underlying epithelial cells and exfoliate either singly or in the form of sheet. This is associated to provide protection by removing silty depositions, pathogens, and debris along with exfoliated keratinized cells/sheets periodically to keep the skin surface clean. Mucogenic epidermis is equipped with the mucous goblet cells and the club cells. Nevertheless, these cells are not discernible in the keratinized structures. This suggests an inverse relationship between mucogenesis and keratinization in the epidermis of the fish. The mucogenic epidermis is involved in the secretion of different classes of glycoproteins. These include glycoproteins with oxidizable vicinal diols, glycoproteins with O-sulphate esters and glycoproteins with sialic acid residues without O-acyl substitution. Secretion of these glycoproteins on the surface are associated to control the acidity of the acidic glycoproteins, to protect the skin surface against bacterial, viral infection and other pathogens, and help in lubrication to protect against abrasion during burrowing. Epidermal keratinization and glycoprotein characterization are associated with the physiological adaptations in relation to the characteristic habit and habitat of the fish.
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Monitoring changing cellular characteristics during the development of a fin cell line from Cyprinus carpio. Comp Biochem Physiol B Biochem Mol Biol 2018; 225:1-12. [PMID: 29960082 DOI: 10.1016/j.cbpb.2018.06.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 06/11/2018] [Accepted: 06/20/2018] [Indexed: 11/21/2022]
Abstract
The establishment and in-depth characterization of a novel continuous cell line derived from fin tissue of common carp (Cyprinus carpio), CCApin, is reported. The cells of the cell line could be propagated in Leibovitz's L-15 medium containing 15% foetal calf serum and 0.5% carp serum for >150 passages during the last 24 months, with a stable fast growth. Furthermore, antibody staining indicated that cell types obtained in primary cultures, containing the epithelial stem-cell marker tumorprotein 63, were different from cells in long-term cell cultures, containing tight junction protein zona occludens 1 and cytokeratin 7. These observations suggest a switch of dominant cell types. Molecular analysis of gene expression profiles of caudal fin tissue and CCApin cells showed that genes relevant in epithelial cells but also in mesenchymal cells were expressed. However, during cultivation of CCApin a set of very steadily expressed, primarily mesenchymal genes like collagen 1 alpha 1, fibronectin or cadherin 2 was found. In summary, the long-term cell culture could be described as a stably growing epithelial population with some mesenchymal features. There are several application possibilities, especially for virus susceptibility studies, e.g. cyprinid herpesvirus-3 (CyHV-3). The study leads to a better understanding of molecular and physiological mechanisms of in vitro fish cell cultures.
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12
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Abstract
The evolution of keratins was closely linked to the evolution of epithelia and epithelial appendages such as hair. The characterization of keratins in model species and recent comparative genomics studies have led to a comprehensive scenario for the evolution of keratins including the following key events. The primordial keratin gene originated as a member of the ancient gene family encoding intermediate filament proteins. Gene duplication and changes in the exon-intron structure led to the origin of type I and type II keratins which evolved further by nucleotide sequence modifications that affected both the amino acid sequences of the encoded proteins and the gene expression patterns. The diversification of keratins facilitated the emergence of new and epithelium type-specific properties of the cytoskeleton. In a common ancestor of reptiles, birds, and mammals, a rise in the number of cysteine residues facilitated extensive disulfide bond-mediated cross-linking of keratins in claws. Subsequently, these cysteine-rich keratins were co-opted for an additional function in epidermal follicular structures that evolved into hair, one of the key events in the evolution of mammals. Further diversification of keratins occurred during the evolution of the complex multi-layered organisation of hair follicles. Thus, together with the evolution of other structural proteins, epithelial patterning mechanisms, and development programmes, the evolution of keratins underlied the evolution of the mammalian integument.
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Affiliation(s)
- Leopold Eckhart
- Research Division of Biology and Pathobiology of the Skin, Department of Dermatology, Medical University of Vienna, Vienna, Austria.
| | - Florian Ehrlich
- Research Division of Biology and Pathobiology of the Skin, Department of Dermatology, Medical University of Vienna, Vienna, Austria
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Suzuki KIT, Suzuki M, Shigeta M, Fortriede JD, Takahashi S, Mawaribuchi S, Yamamoto T, Taira M, Fukui A. Clustered Xenopus keratin genes: A genomic, transcriptomic, and proteomic analysis. Dev Biol 2016; 426:384-392. [PMID: 27842699 DOI: 10.1016/j.ydbio.2016.10.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 10/21/2016] [Accepted: 10/26/2016] [Indexed: 01/21/2023]
Abstract
Keratin genes belong to the intermediate filament superfamily and their expression is altered following morphological and physiological changes in vertebrate epithelial cells. Keratin genes are divided into two groups, type I and II, and are clustered on vertebrate genomes, including those of Xenopus species. Various keratin genes have been identified and characterized by their unique expression patterns throughout ontogeny in Xenopus laevis; however, compilation of previously reported and newly identified keratin genes in two Xenopus species is required for our further understanding of keratin gene evolution, not only in amphibians but also in all terrestrial vertebrates. In this study, 120 putative type I and II keratin genes in total were identified based on the genome data from two Xenopus species. We revealed that most of these genes are highly clustered on two homeologous chromosomes, XLA9_10 and XLA2 in X. laevis, and XTR10 and XTR2 in X. tropicalis, which are orthologous to those of human, showing conserved synteny among tetrapods. RNA-Seq data from various embryonic stages and adult tissues highlighted the unique expression profiles of orthologous and homeologous keratin genes in developmental stage- and tissue-specific manners. Moreover, we identified dozens of epidermal keratin proteins from the whole embryo, larval skin, tail, and adult skin using shotgun proteomics. In light of our results, we discuss the radiation, diversification, and unique expression of the clustered keratin genes, which are closely related to epidermal development and terrestrial adaptation during amphibian evolution, including Xenopus speciation.
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Affiliation(s)
- Ken-Ichi T Suzuki
- Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan.
| | - Miyuki Suzuki
- Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Mitsuki Shigeta
- Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Joshua D Fortriede
- Xenbase, Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Shuji Takahashi
- Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Shuuji Mawaribuchi
- Kitasato Institute for Life Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Takashi Yamamoto
- Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Masanori Taira
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Akimasa Fukui
- Laboratory of Tissue and Polymer Sciences, Faculty of Advanced Life Science, Hokkaido University, N10W8, Sapporo 060-0810, Japan.
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Alibardi L. The Process of Cornification Evolved From the Initial Keratinization in the Epidermis and Epidermal Derivatives of Vertebrates: A New Synthesis and the Case of Sauropsids. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2016; 327:263-319. [DOI: 10.1016/bs.ircmb.2016.06.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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15
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Peter A, Khandekar S, Deakin JE, Stick R. A peculiar lamin in a peculiar mammal: Expression of lamin LIII in platypus (Ornithorhynchus anatinus). Eur J Cell Biol 2015. [PMID: 26213206 DOI: 10.1016/j.ejcb.2015.07.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Platypus (Ornithorhynchus anatinus) holds a unique phylogenetic position at the base of the mammalian lineage due to an amalgamation of mammalian and sauropsid-like features. Here we describe the set of four lamin genes for platypus. Lamins are major components of the nuclear lamina, which constitutes a main component of the nucleoskeleton and is involved in a wide range of nuclear functions. Vertebrate evolution was accompanied by an increase in the number of lamin genes from a single gene in their closest relatives, the tunicates and cephalochordates, to four genes in the vertebrate lineage. Of the four genes the LIII gene is characterized by the presence of two alternatively spliced CaaX-encoding exons. In amphibians and fish LIII is the major lamin protein in oocytes and early embryos. The LIII gene is conserved throughout the vertebrate lineage, with the notable exception of marsupials and placental mammals, which have lost the LIII gene. Here we show that platypus has retained an LIII gene, albeit with a significantly altered structure and with a radically different expression pattern. The platypus LIII gene contains only a single CaaX-encoding exon and the head domain together with coil 1a and part of coil1b of the platypus LIII protein is replaced by a novel short non-helical N-terminus. It is expressed exclusively in the testis. These features resemble those of male germ cell-specific lamins in placental mammals, in particular those of lamin C2. Our data suggest (i) that the specific functions of LIII, which it fulfills in all other vertebrates, is no longer required in mammals and (ii) once it had been freed from these functions has undergone structural alterations and has adopted a new functionality in monotremes.
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Affiliation(s)
- Annette Peter
- Department of Cell Biology, FB2, University of Bremen, P.O. Box 33 04 40, 28334 Bremen, Germany
| | - Shaunak Khandekar
- Cellular and Molecular Pharmacology, Louvain Drug Research Institute, Université catholique de Louvain, avenue E. Mounier 73 bte B1.73.05, B-1200 Brussels, Belgium.
| | - Janine E Deakin
- Research School of Biology, ANU College of Medicine, Biology and Environment, Canberra, Australia.
| | - Reimer Stick
- Department of Cell Biology, FB2, University of Bremen, P.O. Box 33 04 40, 28334 Bremen, Germany.
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Groh KJ, Suter MJF. Stressor-induced proteome alterations in zebrafish: a meta-analysis of response patterns. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2015; 159:1-12. [PMID: 25498419 DOI: 10.1016/j.aquatox.2014.11.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2014] [Revised: 11/05/2014] [Accepted: 11/18/2014] [Indexed: 06/04/2023]
Abstract
Proteomics approaches are being increasingly applied in ecotoxicology on the premise that the identification of specific protein expression changes in response to a particular chemical would allow elucidation of the underlying molecular pathways leading to an adverse effect. This in turn is expected to promote the development of focused testing strategies for specific groups of toxicants. Although both gel-based and gel-free global characterization techniques provide limited proteome coverage, the conclusions regarding the cellular processes affected are still being drawn based on the few changes detected. To investigate how specific the detected responses are, we analyzed a set of studies that characterized proteome alterations induced by various physiological, chemical and biological stressors in zebrafish, a popular model organism. Our analysis highlights several proteins and protein groups, including heat shock and oxidative stress defense proteins, energy metabolism enzymes and cytoskeletal proteins, to be most frequently identified as responding to diverse stressors. In contrast, other potentially more specifically responding protein groups are detected much less frequently. Thus, zebrafish proteome responses to stress reported by different studies appear to depend mostly on the level of stress rather than on the specific stressor itself. This suggests that the most broadly used current proteomics technologies do not provide sufficient proteome coverage to allow in-depth investigation of specific mechanisms of toxicant action. We suggest that the results of any differential proteomics experiment performed with zebrafish should be interpreted keeping in mind the list of the most frequent responders that we have identified. Similar reservations should apply to any other species where proteome responses are analyzed by global proteomics methods. Careful consideration of the reliability and significance of observed changes is necessary in order not to over-interpret the experimental results and to prevent the proliferation of false positive linkages between the chemical and the cellular functions it perturbs. We further discuss the implications of the identified "top lists" of frequently responding proteins and protein families, and suggest further directions for proteomics research in ecotoxicology. Apart from improving the proteome coverage, further research should focus on defining the significance of the observed stress response patterns for organism phenotypes and on searching for common upstream regulators that can be targeted by specific assays.
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Affiliation(s)
- Ksenia J Groh
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland; ETH Zürich, Swiss Federal Institute of Technology, Department of Chemistry and Applied Biosciences, 8093 Zürich, Switzerland.
| | - Marc J-F Suter
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland; ETH Zürich, Swiss Federal Institute of Technology, Department of Environmental Systems Science, 8092 Zürich, Switzerland
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17
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Peter A, Stick R. Evolutionary aspects in intermediate filament proteins. Curr Opin Cell Biol 2015; 32:48-55. [PMID: 25576801 DOI: 10.1016/j.ceb.2014.12.009] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 11/05/2014] [Accepted: 12/19/2014] [Indexed: 01/08/2023]
Abstract
Intermediate filament (IF) proteins, together with tubulins and actins, constitute the majority of cytoskeletal proteins in metazoans. Proteins of the IF family fulfil increasingly diverse functions but share common structural features. Phylogenetic analysis within the metazoan lineage traces back their origin to a common lamin-like ancestor. Major steps in lamin evolution occurred at the base of the vertebrate radiation, while cytoplasmic IF protein subfamilies evolved independently in the major metazoan lineages.
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Affiliation(s)
- Annette Peter
- Department of Cell Biology, Faculty of Biology and Chemistry, University of Bremen, Germany
| | - Reimer Stick
- Department of Cell Biology, Faculty of Biology and Chemistry, University of Bremen, Germany.
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18
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Greenwold MJ, Bao W, Jarvis ED, Hu H, Li C, Gilbert MTP, Zhang G, Sawyer RH. Dynamic evolution of the alpha (α) and beta (β) keratins has accompanied integument diversification and the adaptation of birds into novel lifestyles. BMC Evol Biol 2014; 14:249. [PMID: 25496280 PMCID: PMC4264316 DOI: 10.1186/s12862-014-0249-1] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 11/20/2014] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Vertebrate skin appendages are constructed of keratins produced by multigene families. Alpha (α) keratins are found in all vertebrates, while beta (β) keratins are found exclusively in reptiles and birds. We have studied the molecular evolution of these gene families in the genomes of 48 phylogenetically diverse birds and their expression in the scales and feathers of the chicken. RESULTS We found that the total number of α-keratins is lower in birds than mammals and non-avian reptiles, yet two α-keratin genes (KRT42 and KRT75) have expanded in birds. The β-keratins, however, demonstrate a dynamic evolution associated with avian lifestyle. The avian specific feather β-keratins comprise a large majority of the total number of β-keratins, but independently derived lineages of aquatic and predatory birds have smaller proportions of feather β-keratin genes and larger proportions of keratinocyte β-keratin genes. Additionally, birds of prey have a larger proportion of claw β-keratins. Analysis of α- and β-keratin expression during development of chicken scales and feathers demonstrates that while α-keratins are expressed in these tissues, the number and magnitude of expressed β-keratin genes far exceeds that of α-keratins. CONCLUSIONS These results support the view that the number of α- and β-keratin genes expressed, the proportion of the β-keratin subfamily genes expressed and the diversification of the β-keratin genes have been important for the evolution of the feather and the adaptation of birds into multiple ecological niches.
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Affiliation(s)
- Matthew J Greenwold
- />Department of Biological Sciences, University of South Carolina, Columbia, South Carolina USA
| | - Weier Bao
- />Department of Biological Sciences, University of South Carolina, Columbia, South Carolina USA
| | - Erich D Jarvis
- />Department of Neurobiology, Howard Hughes Medical Institute and Duke University Medical Center, Durham, NC 27710 USA
| | - Haofu Hu
- />China National Genebank, BGI-Shenzhen, Shenzhen, 518083 China
| | - Cai Li
- />China National Genebank, BGI-Shenzhen, Shenzhen, 518083 China
- />Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - M Thomas P Gilbert
- />Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
- />Trace and Environmental DNA Laboratory, Department of Environment and Agriculture, Curtin University, Perth, Western Australia 6102 Australia
| | - Guojie Zhang
- />China National Genebank, BGI-Shenzhen, Shenzhen, 518083 China
- />Centre for Social Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark
| | - Roger H Sawyer
- />Department of Biological Sciences, University of South Carolina, Columbia, South Carolina USA
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Khan I, Maldonado E, Vasconcelos V, O'Brien SJ, Johnson WE, Antunes A. Mammalian keratin associated proteins (KRTAPs) subgenomes: disentangling hair diversity and adaptation to terrestrial and aquatic environments. BMC Genomics 2014; 15:779. [PMID: 25208914 PMCID: PMC4180150 DOI: 10.1186/1471-2164-15-779] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 07/30/2014] [Indexed: 11/24/2022] Open
Abstract
Background Adaptation of mammals to terrestrial life was facilitated by the unique vertebrate trait of body hair, which occurs in a range of morphological patterns. Keratin associated proteins (KRTAPs), the major structural hair shaft proteins, are largely responsible for hair variation. Results We exhaustively characterized the KRTAP gene family in 22 mammalian genomes, confirming the existence of 30 KRTAP subfamilies evolving at different rates with varying degrees of diversification and homogenization. Within the two major classes of KRTAPs, the high cysteine (HS) subfamily experienced strong concerted evolution, high rates of gene conversion/recombination and high GC content. In contrast, high glycine-tyrosine (HGT) KRTAPs showed evidence of positive selection and low rates of gene conversion/recombination. Species with more hair and of higher complexity tended to have more KRATP genes (gene expansion). The sloth, with long and coarse hair, had the most KRTAP genes (175 with 141 being intact). By contrast, the “hairless” dolphin had 35 KRTAPs and the highest pseudogenization rate (74% relative to the 19% mammalian average). Unique hair-related phenotypes, such as scales (armadillo) and spines (hedgehog), were correlated with changes in KRTAPs. Gene expression variation probably also influences hair diversification patterns, for example human have an identical KRTAP repertoire as apes, but much less hair. Conclusions We hypothesize that differences in KRTAP gene repertoire and gene expression, together with distinct rates of gene conversion/recombination, pseudogenization and positive selection, are likely responsible for micro and macro-phenotypic hair diversification among mammals in response to adaptations to ecological pressures. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-779) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | - Agostinho Antunes
- CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Rua dos Bragas 177, 4050-123 Porto, Portugal.
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20
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Ng CS, Wu P, Fan WL, Yan J, Chen CK, Lai YT, Wu SM, Mao CT, Chen JJ, Lu MYJ, Ho MR, Widelitz RB, Chen CF, Chuong CM, Li WH. Genomic organization, transcriptomic analysis, and functional characterization of avian α- and β-keratins in diverse feather forms. Genome Biol Evol 2014; 6:2258-73. [PMID: 25152353 PMCID: PMC4202321 DOI: 10.1093/gbe/evu181] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Feathers are hallmark avian integument appendages, although they were also present on theropods. They are composed of flexible corneous materials made of α- and β-keratins, but their genomic organization and their functional roles in feathers have not been well studied. First, we made an exhaustive search of α- and β-keratin genes in the new chicken genome assembly (Galgal4). Then, using transcriptomic analysis, we studied α- and β-keratin gene expression patterns in five types of feather epidermis. The expression patterns of β-keratin genes were different in different feather types, whereas those of α-keratin genes were less variable. In addition, we obtained extensive α- and β-keratin mRNA in situ hybridization data, showing that α-keratins and β-keratins are preferentially expressed in different parts of the feather components. Together, our data suggest that feather morphological and structural diversity can largely be attributed to differential combinations of α- and β-keratin genes in different intrafeather regions and/or feather types from different body parts. The expression profiles provide new insights into the evolutionary origin and diversification of feathers. Finally, functional analysis using mutant chicken keratin forms based on those found in the human α-keratin mutation database led to abnormal phenotypes. This demonstrates that the chicken can be a convenient model for studying the molecular biology of human keratin-based diseases.
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Affiliation(s)
- Chen Siang Ng
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Ping Wu
- Department of Pathology, Keck School of Medicine, University of Southern California
| | - Wen-Lang Fan
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Jie Yan
- Department of Pathology, Keck School of Medicine, University of Southern California Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, China
| | - Chih-Kuan Chen
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan
| | - Yu-Ting Lai
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Siao-Man Wu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Chi-Tang Mao
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan Molecular Biology of Agricultural Sciences, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
| | - Jun-Jie Chen
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Mei-Yeh Jade Lu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Meng-Ru Ho
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Randall B Widelitz
- Department of Pathology, Keck School of Medicine, University of Southern California
| | - Chih-Feng Chen
- Department of Animal Science, National Chung Hsing University, Taichung, Taiwan Center for the Integrative and Evolutionary Galliformes Genomics (iEGG Center), National Chung Hsing University, Taichung, Taiwan
| | - Cheng-Ming Chuong
- Department of Pathology, Keck School of Medicine, University of Southern California Center for the Integrative and Evolutionary Galliformes Genomics (iEGG Center), National Chung Hsing University, Taichung, Taiwan
| | - Wen-Hsiung Li
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan Department of Ecology and Evolution, University of Chicago
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21
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Schilf P, Peter A, Hurek T, Stick R. Lamins of the sea lamprey (Petromyzon marinus) and the evolution of the vertebrate lamin protein family. Eur J Cell Biol 2014; 93:308-21. [DOI: 10.1016/j.ejcb.2014.06.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 06/23/2014] [Accepted: 06/25/2014] [Indexed: 10/25/2022] Open
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22
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Karabinos A. The cephalochordate Branchiostoma genome contains 26 intermediate filament (IF) genes: Implications for evolution of chordate IF proteins. Eur J Cell Biol 2013; 92:295-302. [DOI: 10.1016/j.ejcb.2013.10.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Revised: 09/17/2013] [Accepted: 10/10/2013] [Indexed: 11/16/2022] Open
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Abstract
Lamins are the major components of the nuclear lamina, a filamentous layer found at the interphase between chromatin and the inner nuclear membrane. The lamina supports the nuclear envelope and provides anchorage sites for chromatin. Lamins and their associated proteins are required for most nuclear activities, mitosis, and for linking the nucleoskeleton to the network of cytoskeletal filaments. Mutations in lamins and their associated proteins give rise to a wide range of diseases, collectively called laminopathies. This review focuses on the evolution of the lamin protein family. Evolution from basal metazoans to man will be described on the basis of protein sequence comparisons and analyses of their gene structure. Lamins are the founding members of the family of intermediate filament proteins. How genes encoding cytoplasmic IF proteins could have arisen from the archetypal lamin gene progenitor, can be inferred from a comparison of the respective gene structures. The lamin/IF protein family seems to be restricted to the metazoans. In general, invertebrate genomes harbor only a single lamin gene encoding a B-type lamin. The archetypal lamin gene structure found in basal metazoans is conserved up to the vertebrate lineage. The completely different structure of lamin genes in Caenorhabditis and Drosophila are exceptions rather than the rule within their systematic groups. However, variation in the length of the coiled-coil forming central domain might be more common than previously anticipated. The increase in the number of lamin genes in vertebrates can be explained by two rounds of genome duplication. The origin of lamin A by exon shuffling might explain the processing of prelamin A to the mature non-isoprenylated form of lamin A. By alternative splicing the number of vertebrate lamin proteins has increased even further. Lamin C, an alternative splice form of the LMNA gene, is restricted to mammals. Amphibians and mammals express germline-specific lamins that differ in their protein structure from that of somatic lamins. Evidence is provided that there exist lamin-like proteins outside the metazoan lineage.
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Affiliation(s)
- Annette Peter
- Department for Cell Biology, University of Bremen, Bremen, Germany
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24
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Linard B, Nguyen NH, Prosdocimi F, Poch O, Thompson JD. EvoluCode: Evolutionary Barcodes as a Unifying Framework for Multilevel Evolutionary Data. Evol Bioinform Online 2011; 8:61-77. [PMID: 22267905 PMCID: PMC3256995 DOI: 10.4137/ebo.s8814] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Evolutionary systems biology aims to uncover the general trends and principles governing the evolution of biological networks. An essential part of this process is the reconstruction and analysis of the evolutionary histories of these complex, dynamic networks. Unfortunately, the methodologies for representing and exploiting such complex evolutionary histories in large scale studies are currently limited. Here, we propose a new formalism, called EvoluCode (Evolutionary barCode), which allows the integration of different evolutionary parameters (eg, sequence conservation, orthology, synteny …) in a unifying format and facilitates the multilevel analysis and visualization of complex evolutionary histories at the genome scale. The advantages of the approach are demonstrated by constructing barcodes representing the evolution of the complete human proteome. Two large-scale studies are then described: (i) the mapping and visualization of the barcodes on the human chromosomes and (ii) automatic clustering of the barcodes to highlight protein subsets sharing similar evolutionary histories and their functional analysis. The methodologies developed here open the way to the efficient application of other data mining and knowledge extraction techniques in evolutionary systems biology studies. A database containing all EvoluCode data is available at: http://lbgi.igbmc.fr/barcodes.
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Affiliation(s)
- Benjamin Linard
- Laboratoire De Bioinformatique Et Génomique Intégratives, Institut de Génétique et de Biologie Moléculaire et Cellulaire CNRS/INSERM/UDS, Illkirch, France
| | - Ngoc Hoan Nguyen
- Laboratoire De Bioinformatique Et Génomique Intégratives, Institut de Génétique et de Biologie Moléculaire et Cellulaire CNRS/INSERM/UDS, Illkirch, France
| | | | - Olivier Poch
- Laboratoire De Bioinformatique Et Génomique Intégratives, Institut de Génétique et de Biologie Moléculaire et Cellulaire CNRS/INSERM/UDS, Illkirch, France
| | - Julie D. Thompson
- Laboratoire De Bioinformatique Et Génomique Intégratives, Institut de Génétique et de Biologie Moléculaire et Cellulaire CNRS/INSERM/UDS, Illkirch, France
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Vandebergh W, Bossuyt F. Radiation and Functional Diversification of Alpha Keratins during Early Vertebrate Evolution. Mol Biol Evol 2011; 29:995-1004. [DOI: 10.1093/molbev/msr269] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
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26
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Hasebe T, Kajita M, Iwabuchi M, Ohsumi K, Ishizuya-Oka A. Thyroid hormone-regulated expression of nuclear lamins correlates with dedifferentiation of intestinal epithelial cells during Xenopus laevis metamorphosis. Dev Genes Evol 2011; 221:199-208. [PMID: 21866414 DOI: 10.1007/s00427-011-0371-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2011] [Accepted: 07/04/2011] [Indexed: 11/26/2022]
Abstract
In the Xenopus laevis intestine during metamorphosis, which is triggered by thyroid hormone (TH), the adult epithelium develops and replaces the larval one undergoing apoptosis. We have previously shown that progenitor/stem cells of the adult epithelium originate from some differentiated larval epithelial cells. To investigate molecular mechanisms underlying larval epithelial dedifferentiation into the adult progenitor/stem cells, we here focused on nuclear lamin A (LA) and lamin LIII (LIII), whose expression is generally known to be correlated with the state of cell differentiation. We analyzed the spatiotemporal expression of LA and LIII during X. laevis intestinal remodeling by reverse transcription PCR, Western blotting, and immunohistochemistry. At the onset of natural metamorphosis, when the adult epithelial progenitor cells appear as small islets, the expression of LA is down-regulated, but that of LIII is up-regulated only in the islets. Then, as the adult progenitor cells differentiate, the expression of LA is up-regulated, whereas that of LIII is down-regulated in the adult cells. As multiple intestinal folds form, adult epithelial cells positive for LIII become restricted only to the troughs of the folds. In addition, we have shown that TH up- or down-regulates the expression of these lamins in the premetamorphic intestine as during natural metamorphosis. These results indicate that TH-regulated expression of LA and LIII closely correlates with dedifferentiation of the epithelial cells in the X. laevis intestine, suggesting the involvement of the lamins in the process of dedifferentiation during amphibian metamorphosis.
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Affiliation(s)
- Takashi Hasebe
- Department of Biology, Nippon Medical School, 2-297-2 Kosugi-cho, Nakahara-ku, Kawasaki, Kanagawa 211-0063, Japan
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Greenwold MJ, Sawyer RH. Linking the molecular evolution of avian beta (β) keratins to the evolution of feathers. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2011; 316:609-16. [DOI: 10.1002/jez.b.21436] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2011] [Revised: 06/20/2011] [Accepted: 07/25/2011] [Indexed: 11/12/2022]
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Molecular characterization of a novel type II keratin gene (sseKer3) in the Senegalese sole (Solea senegalensis): Differential expression of keratin genes by salinity. Comp Biochem Physiol B Biochem Mol Biol 2011; 160:15-23. [DOI: 10.1016/j.cbpb.2011.04.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2011] [Revised: 04/14/2011] [Accepted: 04/15/2011] [Indexed: 01/19/2023]
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29
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Rufino-Palomares E, Reyes-Zurita FJ, Fuentes-Almagro CA, de la Higuera M, Lupiáñez JA, Peragón J. Proteomics in the liver of gilthead sea bream (Sparus aurata
) to elucidate the cellular response induced by the intake of maslinic acid. Proteomics 2011; 11:3312-25. [DOI: 10.1002/pmic.201000271] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2010] [Revised: 04/08/2011] [Accepted: 05/12/2011] [Indexed: 02/04/2023]
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30
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Suzuki KIT, Kashiwagi K, Ujihara M, Marukane T, Tazaki A, Watanabe K, Mizuno N, Ueda Y, Kondoh H, Kashiwagi A, Mochii M. Characterization of a novel type I keratin gene and generation of transgenic lines with fluorescent reporter genes driven by its promoter/enhancer in Xenopus laevis. Dev Dyn 2010; 239:3172-81. [PMID: 20941778 DOI: 10.1002/dvdy.22451] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/07/2010] [Indexed: 11/08/2022] Open
Abstract
We investigated the characteristics of a novel type I keratin gene in Xenopus laevis during ontogenesis. The transcript was first detected in the posterior region at the late neurula stage, and then restricted to the fin and external gill during embryogenesis. To examine the transcriptional regulation of the keratin gene in vivo, we generated transgenic lines with fluorescent reporter genes driven by its 4.2-kb upstream sequence. The promoter/enhancer activity recapitulated the endogenous gene expression during embryogenesis. Sequential deletion analyses revealed that the regions proximal to the promoter were essential for fin-specific expression. Reporter expression was detected in various organs, including the fin and gill. In particular, robust expression was observed in the developing limbs and gill. The reporter fluorescence rapidly decreased with internal gill resorption during metamorphosis. The transgenic lines carrying the promoter/enhancer should represent valuable tools for elucidating the formation, development and resorption of various organs, especially the gill.
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Affiliation(s)
- Ken-ichi T Suzuki
- Department of Biological Science, Graduate School of Science, Hiroshima University, Hiroshima, Japan
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31
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von Moeller F, Barendziak T, Apte K, Goldberg MW, Stick R. Molecular characterization of Xenopus lamin LIV reveals differences in the lamin composition of sperms in amphibians and mammals. Nucleus 2010; 1:85-95. [PMID: 21327107 PMCID: PMC3035121 DOI: 10.4161/nucl.1.1.10517] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2009] [Revised: 11/04/2009] [Accepted: 11/04/2009] [Indexed: 02/06/2023] Open
Abstract
Lamins are nuclear intermediate filament proteins. They are involved in most nuclear activities and are essential for retaining the mechano-elastic properties of the nucleus. Somatic cells of vertebrates express lamins A, B1 and B2 while lamin LIII, a major component of the amphibian oocyte lamina is absent in mammals. The organization of the lamina of germ cells differs significantly from that of somatic cells. Mammalian spermatogenic cells express two short lamins, C2 and B3, that are splice isoforms of lamin A and B2, respectively. Here we identify the previously described Xenopus lamin LIV as splice variant of the lamin LIII gene. LIV contains 40 extra residues in coil 2A of the rod domain, which results in altered assembly properties. Xenopus lamin LIV and mammalian B3 assemble into short structures rather than into long IF-like filaments. Expression of lamin LIV is restricted to male germ cells suggesting that it might be the functional equivalent of mammalian lamin B3. We provide evidence that lamins C2 and B3 are restricted to the mammalian lineage and describe the lamin composition of Xenopus sperm. Our results show that the evolution of germ cell-specific lamins followed separate and distinctly different paths in amphibians and mammals.
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Affiliation(s)
| | - Tanja Barendziak
- Department of Cell Biology; University of Bremen; Bremen, Germany
| | - Ketaki Apte
- Department of Cell Biology; University of Bremen; Bremen, Germany
| | - Martin W Goldberg
- School of Biological and Biomedical Sciences; The University of Durham; Durham, UK
| | - Reimer Stick
- Department of Cell Biology; University of Bremen; Bremen, Germany
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Peter A, Stick R. Ectopic expression of prelamin A in early Xenopus embryos induces apoptosis. Eur J Cell Biol 2009; 87:879-91. [PMID: 18675490 DOI: 10.1016/j.ejcb.2008.06.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2008] [Revised: 05/23/2008] [Accepted: 06/11/2008] [Indexed: 01/24/2023] Open
Abstract
Lamin proteins are components of metazoan cell nuclei. During evolution, two classes of lamin proteins evolved, A- and B-type lamins. B-type lamins are expressed in nearly all cell types and in all developmental stages and are thought to be indispensable for cellular survival. In contrast, A-type lamins have a more restricted expression pattern. They are expressed in differentiated cells and appear late in embryogenesis. In the earliest steps of mammalian development, A-type lamins are present in oocytes, pronuclei and during the first cleavage stages of the developing embryo. But latest after the 16-cell stage, A-type lamin proteins are not any longer detectable in embryonic cells. Amphibian oocytes and early embryos do not express lamin A. Moreover, extracts of Xenopus oocytes and eggs have the ability to selectively remove A-type lamins from somatic nuclei. This observation and the restricted expression pattern suggest that the presence of lamin A might interfere with developmental processes in the early phase of embryogenesis. To test this, we ectopically expressed lamin A during early embryonic development of Xenopus laevis by microinjection of synthetic mRNA. Here, we show that introducing mature lamin A does not interfere with normal development. However, expression of prelamin A or lamin A variants that cannot be fully processed cause severe disturbances and lead to apoptosis during gastrulation. The toxic effect is due to lack of the conversion of prenylated prelamin A to its mature form. Remarkably, even a cytoplasmic prelamin A variant that is excluded from the nucleus drives embryos into apoptosis.
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Affiliation(s)
- Annette Peter
- Department of Cell Biology, University of Bremen, P.O. Box 33 04 40, D-28334 Bremen, Germany
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Identification of reptilian genes encoding hair keratin-like proteins suggests a new scenario for the evolutionary origin of hair. Proc Natl Acad Sci U S A 2008; 105:18419-23. [PMID: 19001262 DOI: 10.1073/pnas.0805154105] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The appearance of hair is one of the main evolutionary innovations in the amniote lineage leading to mammals. The main components of mammalian hair are cysteine-rich type I and type II keratins, also known as hard alpha-keratins or "hair keratins." To determine the evolutionary history of these important structural proteins, we compared the genomic loci of the human hair keratin genes with the homologous loci of the chicken and of the green anole lizard Anolis carolinenis. The genome of the chicken contained one type II hair keratin-like gene, and the lizard genome contained two type I and four type II hair keratin-like genes. Orthology of the latter genes and mammalian hair keratins was supported by gene locus synteny, conserved exon-intron organization, and amino acid sequence similarity of the encoded proteins. The lizard hair keratin-like genes were expressed most strongly in the digits, indicating a role in claw formation. In addition, we identified a novel group of reptilian cysteine-rich type I keratins that lack homologues in mammals. Our data show that cysteine-rich alpha-keratins are not restricted to mammals and suggest that the evolution of mammalian hair involved the co-option of pre-existing structural proteins.
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Infante C, Manchado M, Asensio E, Cañavate JP. Molecular characterization, gene expression and dependence on thyroid hormones of two type I keratin genes (sseKer1 and sseKer2) in the flatfish Senegalese sole (Solea senegalensis Kaup). BMC DEVELOPMENTAL BIOLOGY 2007; 7:118. [PMID: 17956602 PMCID: PMC2174949 DOI: 10.1186/1471-213x-7-118] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2007] [Accepted: 10/23/2007] [Indexed: 12/22/2022]
Abstract
BACKGROUND Keratins make up the largest subgroup of intermediate filaments, and, in chordates, represent the most abundant proteins in epithelial cells. They have been associated with a wide range of functions in the cell, but little information is still available about their expression profile and regulation during flatfish metamorphosis. Senegalese sole (Solea senegalensis) is a commercially important flatfish in which no keratin gene has been described yet. RESULTS The development of large-scale genomics of Senegalese sole has facilitated the identification of two different type I keratin genes referred to as sseKer1 and sseKer2. Main characteristics and sequence identities with other fish and mammal keratins are described. Phylogenetic analyses grouped sseKer1 and sseKer2 in a significant clade with other teleost epidermal type I keratins, and have allowed for the identification of sseKer2 as a novel keratin. The expression profile of both genes was studied during larval development and in tissues using a real-time approach. sseKer1 and sseKer2 mRNA levels were significantly higher in skin than in other tissues examined. During metamorphosis, sseKer1 transcripts increased significantly at first stages, and reduced thereafter. In contrast, sseKer2 mRNA levels did not change during early metamorphosis although a significant drop at metamorphosis climax and late metamorphosis was also detected. To study the possible regulation of sseKer gene expressions by thyroid hormones (THs), larvae were exposed to the goitrogen thiourea (TU). TU-treated larvae exhibited higher sseKer1 and sseKer2 mRNA levels than untreated control at both 11 and 15 days after treatment. Moreover, addition of exogenous T4 hormone to TU-treated larvae restored or even reduced the steady-state levels with respect to the untreated control, demonstrating that expression of both genes is negatively regulated by THs. CONCLUSION We have identified two keratin genes, referred to as sseKer1 and sseKer2, in Senegalese sole. Phylogenetic analyses revealed sseKer2 as a novel keratin. Although they exhibit different expression patterns during larval development, both of them are negatively regulated by THs. The co-regulation by THs could explain the reduction of both keratin transcripts after the metamorphosis climax, suggesting their role in the tissue remodelling processes that occur during metamorphosis.
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Affiliation(s)
- Carlos Infante
- IFAPA Centro El Toruño, Junta de Andalucía, Camino Tiro de pichón s/n, 11500 El Puerto de Santa María, Cádiz, Spain.
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Kim S, Coulombe PA. Intermediate filament scaffolds fulfill mechanical, organizational, and signaling functions in the cytoplasm. Genes Dev 2007; 21:1581-97. [PMID: 17606637 DOI: 10.1101/gad.1552107] [Citation(s) in RCA: 227] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Intermediate filaments (IFs) are cytoskeletal polymers whose protein constituents are encoded by a large family of differentially expressed genes. Owing in part to their properties and intracellular organization, IFs provide crucial structural support in the cytoplasm and nucleus, the perturbation of which causes cell and tissue fragility and accounts for a large number of genetic diseases in humans. A number of additional roles, nonmechanical in nature, have been recently uncovered for IF proteins. These include the regulation of key signaling pathways that control cell survival, cell growth, and vectorial processes including protein targeting in polarized cellular settings. As this discovery process continues to unfold, a rationale for the large size of this family and the context-dependent regulation of its members is finally emerging.
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Affiliation(s)
- Seyun Kim
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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Schaffeld M, Haberkamp M, Schätzlein S, Neumann S, Hunzinger C. A novel and ancient group of type I keratins with members in bichir, sturgeon and gar. Front Zool 2007; 4:16. [PMID: 17553169 PMCID: PMC1896152 DOI: 10.1186/1742-9994-4-16] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2006] [Accepted: 06/06/2007] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Vertebrate epithelial cells typically express a specific set of keratins. In teleosts, keratins are also present in a variety of mesenchymal cells, which usually express vimentin. Significantly, our previous studies revealed that virtually all known teleost keratins evolved independently from those present in terrestrial vertebrates. To further elucidate the evolutionary scenario that led to the large variety of keratins and their complex expression patterns in present day teleosts, we have investigated their presence in bichir, sturgeon and gar. RESULTS We have discovered a novel group of type I keratins with members in all three of these ancient ray-finned fish, but apparently no counterparts are present in any other vertebrate class so far investigated, including the modern teleost fish. From sturgeon and gar we sequenced one and from bichir two members of this novel keratin group. By complementary keratin blot-binding assays and peptide mass fingerprinting using MALDI-TOF mass spectrometry, in sturgeon we were able to assign the sequence to a prominent protein spot, present exclusively in a two-dimensionally separated cytoskeletal preparation of skin, thus identifying it as an epidermally expressed type I keratin. In contrast to the other keratins we have so far sequenced from bichir, sturgeon and gar, these new sequences occupy a rather basal position within the phylogenetic tree of type I keratins, in a close vicinity to the keratins we previously cloned from river lamprey. CONCLUSION Thus, this new K14 group seem to belong to a very ancient keratin branch, whose functional role has still to be further elucidated. Furthermore, the exclusive presence of this keratin group in bichir, sturgeon and gar points to the close phylogenetic relationship of these ray- finned fish, an issue still under debate among taxonomists.
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Affiliation(s)
- Michael Schaffeld
- Institute of Zoology, Johannes-von-Müller-Weg 6, Johannes Gutenberg University, D-55099 Mainz, Germany
| | - Mark Haberkamp
- Institute of Zoology, Johannes-von-Müller-Weg 6, Johannes Gutenberg University, D-55099 Mainz, Germany
| | - Sonja Schätzlein
- Dept. of Gastroenterology, Medical School Hannover, Carl Neuberg Str. 1, K11, E01, R1400, 30629 Hannover, Germany
| | - Sebastian Neumann
- Institute of Zoology, Johannes-von-Müller-Weg 6, Johannes Gutenberg University, D-55099 Mainz, Germany
| | - Christian Hunzinger
- Merck KGaA, Central Services Analytics, Central Product Analytics/Bioanalytics, Frankfurter Str. 250, D-64293 Darmstadt, Germany
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Omary MB, Ku NO, Tao GZ, Toivola DM, Liao J. "Heads and tails" of intermediate filament phosphorylation: multiple sites and functional insights. Trends Biochem Sci 2006; 31:383-94. [PMID: 16782342 DOI: 10.1016/j.tibs.2006.05.008] [Citation(s) in RCA: 221] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2006] [Revised: 05/02/2006] [Accepted: 05/25/2006] [Indexed: 01/19/2023]
Abstract
Intermediate filaments (IFs) are major components of the mammalian cytoskeleton. They are among the most abundant cellular phosphoproteins; their phosphorylation typically involves multiple sites at repeat or unique motifs, preferentially within the "head" or "tail" domains. Phosphorylation and dephosphorylation are essential for the regulation of IF dynamics by modulating the intrinsic properties of IFs: solubility, conformation and filament organization, and, in addition, for the regulation of other IF post-translational modifications. These phosphorylation-regulated properties dictate generalized and context-dependent IF functions that reflect their tissue-specific expression. Most important among IF phosphorylation-mediated functions are the regulation of IF cellular or subcellular compartmentalization, levels and turnover, binding with associated proteins, susceptibility to cell stresses (including apoptosis), tissue-specific functions and IF-associated disease pathogenesis (where IF hyperphosphorylation also serves as a tissue-injury marker).
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Affiliation(s)
- M Bishr Omary
- Department of Medicine, Palo Alto VA Medical Center and Stanford University School of Medicine, 3801 Miranda Avenue, Palo Alto, CA 94304, USA.
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Arbiza L, Dopazo J, Dopazo H. Positive selection, relaxation, and acceleration in the evolution of the human and chimp genome. PLoS Comput Biol 2006; 2:e38. [PMID: 16683019 PMCID: PMC1447656 DOI: 10.1371/journal.pcbi.0020038] [Citation(s) in RCA: 125] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2005] [Accepted: 03/15/2006] [Indexed: 12/05/2022] Open
Abstract
For years evolutionary biologists have been interested in searching for the genetic bases underlying humanness. Recent efforts at a large or a complete genomic scale have been conducted to search for positively selected genes in human and in chimp. However, recently developed methods allowing for a more sensitive and controlled approach in the detection of positive selection can be employed. Here, using 13,198 genes, we have deduced the sets of genes involved in rate acceleration, positive selection, and relaxation of selective constraints in human, in chimp, and in their ancestral lineage since the divergence from murids. Significant deviations from the strict molecular clock were observed in 469 human and in 651 chimp genes. The more stringent branch-site test of positive selection detected 108 human and 577 chimp positively selected genes. An important proportion of the positively selected genes did not show a significant acceleration in rates, and similarly, many of the accelerated genes did not show significant signals of positive selection. Functional differentiation of genes under rate acceleration, positive selection, and relaxation was not statistically significant between human and chimp with the exception of terms related to G-protein coupled receptors and sensory perception. Both of these were over-represented under relaxation in human in relation to chimp. Comparing differences between derived and ancestral lineages, a more conspicuous change in trends seems to have favored positive selection in the human lineage. Since most of the positively selected genes are different under the same functional categories between these species, we suggest that the individual roles of the alternative positively selected genes may be an important factor underlying biological differences between these species. Since the publication of the human and the chimp genomes, one of the major challenges in evolutionary biology has begun to be deciphered: namely, the search for positively selected genes that have shaped humanness. Arbiza and colleagues undertake a genomic-scale search for the genes that have been positively selected in human, in chimp, and in their common ancestral lineage. They conclude that events of positive selection were six times more frequent in chimp than in human, although they do not group under specific functional classes that have been preferentially selected in either species. However, in the comparisons of the evolutionary trends between the ancestral and the descendant lineages, they found that most of the relative differences in common classes show an abundance of positive selection on the human branch. By differentiating positive selection from a relaxation of selective constraints, both producing analogous footprints in the genome, they demonstrate that many of the genes previously thought to have been positively selected correspond to likely cases of relaxation. Finally, they quantify the bias produced by the use of average rate–based approaches to concentrate cases of adaptive evolution in these species.
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Affiliation(s)
- Leonardo Arbiza
- Pharmacogenomics and Comparative Genomics Unit, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain
| | - Joaquín Dopazo
- Functional Genomics Unit, Bioinformatics Department, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain
| | - Hernán Dopazo
- Pharmacogenomics and Comparative Genomics Unit, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain
- * To whom correspondence should be addressed. E-mail:
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Krushna Padhi B, Akimenko MA, Ekker M. Independent expansion of the keratin gene family in teleostean fish and mammals: An insight from phylogenetic analysis and radiation hybrid mapping of keratin genes in zebrafish. Gene 2006; 368:37-45. [PMID: 16297574 DOI: 10.1016/j.gene.2005.09.016] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2005] [Revised: 09/12/2005] [Accepted: 09/29/2005] [Indexed: 12/27/2022]
Abstract
The sequence and chromosomal distribution of keratin genes of zebrafish were compared with that of other fishes and mammals to provide an insight into the evolution of this gene family in vertebrates. By comparative sequence analysis and radiation hybrid mapping, we identified 16 type I and 7 type II keratin genes in the zebrafish genome. This contrasts with mammals, where type I and type II keratin genes are similar in number. The keratin genes are scattered in the fish genome, contrasting with the two clusters of keratin genes in mammalian genomes. Compared to genes from two species of pufferfish, the zebrafish type I keratin genes underwent an expansion by independent tandem duplications. Expression profiles based on EST counts suggest that some of the tandemly duplicated type I keratin genes from zebrafish either underwent sub-functionalization or acquired new expression domains. The chromosomal arrangement of keratins 8, keratin18, and a second type II keratin, as a cluster of three genes, has remained conserved in vertebrate evolution, except for duplication of the three-gene cluster in some teleosts. This contrasts with other members of the keratin gene family, which diverged independently between fish and mammals.
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Affiliation(s)
- Bhaja Krushna Padhi
- Ottawa Health Research Institute, 725 Parkdale Avenue, Ottawa, ON, Canada K1Y 4E9
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Schaffeld M, Schultess J. Genes coding for intermediate filament proteins closely related to the hagfish "thread keratins (TK)" alpha and gamma also exist in lamprey, teleosts and amphibians. Exp Cell Res 2006; 312:1447-62. [PMID: 16494865 DOI: 10.1016/j.yexcr.2006.01.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2005] [Revised: 01/09/2006] [Accepted: 01/10/2006] [Indexed: 01/16/2023]
Abstract
The "thread keratins (TK)" alpha and gamma so far have been considered highly specialized intermediate filament (IF) proteins restricted to hagfish. From lamprey, we now have sequenced five novel IF proteins closely related to TKalpha and TKgamma, respectively. Moreover, we have detected corresponding sequences in EST and genomic databases of teleosts and amphibians. The structure of the TKalpha genes and the positions of their deduced amino acid sequences in a phylogenetic tree clearly support their classification as type II keratins. The genes encoding TKgamma show a structure typical for type III IF proteins, whereas their positions in phylogenetic trees favor a close relationship to the type I keratins. Considering that most keratin-like sequences detected in the lancelet also exhibit a gene structure typical for type III IF proteins, it seems likely that the keratin gene(s) originated from an ancient type III IF protein gene. According to EST analyses, the expression of the thread keratins in teleost fish and amphibians may be particularly restricted to larval stages, which, in conjunction with the observed absence of TKalpha and TKgamma genes in any of the available Amniota databases, indicates a thread keratin function closely related to larval development in an aquatic environment.
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Affiliation(s)
- Michael Schaffeld
- Institute of Zoology, Johannes-von-Müller-Weg 6, Johannes Gutenberg University, D-55099 Mainz, Germany.
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Zimek A, Weber K. The organization of the keratin I and II gene clusters in placental mammals and marsupials show a striking similarity. Eur J Cell Biol 2005; 85:83-9. [PMID: 16439307 DOI: 10.1016/j.ejcb.2005.10.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2005] [Accepted: 10/04/2005] [Indexed: 01/10/2023] Open
Abstract
The genomic database for a marsupial, the opossum Monodelphis domestica, is highly advanced. This allowed a complete analysis of the keratin I and keratin II gene cluster with some 30 genes in each cluster as well as a comparison with the human keratin clusters. Human and marsupial keratin gene clusters have an astonishingly similar organization. As placental mammals and marsupials are sister groups a corresponding organization is also expected for the archetype mammal. Since hair is a mammalian acquisition the following features of the cluster refer to its origin. In both clusters hair keratin genes arose at an interior position. While we do not know from which epithelial keratin genes the first hair keratins type-I and -II genes evolved, subsequent gene duplications gave rise to a subdomain of the clusters with many neighboring hair keratin genes. A second subdomain accounts in both clusters for 4 neighboring genes encoding the keratins of the inner root sheath (irs) keratins. Finally the hair keratin gene subdomain in the type-I gene cluster is interrupted after the second gene by a region encoding numerous genes for the high/ultrahigh sulfur hair keratin-associated proteins (KAPs). We also propose a tentative synteny relation of opossum and human genes based on maximal sequence conservation of the encoded keratins. The keratin gene clusters of the opossum seem to lack pseudogenes and display a slightly increased number of genes. Opossum keratin genes are usually longer than their human counterparts and also show longer intergenic distances.
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Affiliation(s)
- Alexander Zimek
- Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany
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