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Characterization of a novel fructosyltransferase InuCA from Lactobacillus crispatus that attaches to the cell surface by electrostatic interaction. Appl Environ Microbiol 2021; 88:e0239921. [PMID: 34910558 DOI: 10.1128/aem.02399-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Fructosyltransferases (FTases), a group of carbohydrate-active enzymes, synthesize fructooligosaccharides (FOS) and fructans, which are promising prebiotics for human health. Here we originally identified a novel FTase InuCA from L. crispatus, a dominant species in the vaginal microbiotas of human. InuCA was characterized by a shortest C-terminus and the highest isoelectric point among the reported Lactobacillus FTases. InuCA was an inulosucrase and produced a serial of FOS using sucrose as substrate at a moderate temperature. Surprisingly, the C-terminal deletion mutant synthesized oligosaccharides with fructosyl chain longer than that of the wild type, suggesting that the C-terminal part blocked the binding of long-chain receptor. Moreover, InuCA bound to the cell surface by electrostatic interaction, which was dependent on the environmental pH and represented a distinctive binding mode in FTases. The catalytic and structural properties of InuCA will be contributed to the FTases engineering and the knowledge of the adaptation of L. crispatus in the vaginal environment. Importance L. crispatus is one of the most important species in human vaginal microbiotas and its persistence is strongly negatively correlated with the vaginal diseases. Our research reveals that a novel inulosucrase InuCA is present in L. cirspatus. InuCA keeps the ability to synthesize prebiotic fructo-oligosaccharides, although it lacks a large part of the C-terminal region compared to other FTases. Remarkably, the short C-terminus of InuCA blocks the transfructosylation activity for producing oligosaccharides with longer chain, which is meaningful to the directional modification of FTases and the oligosaccharide products. Besides the catalytic activity, InuCA is anchored on the cell surface dependent on the environmental pH and may be also involved in the adhesion of L. crispatus to the vaginal epithelial cells. Since L. crispatus plays an essential role in the normal vaginal micro-ecosystem, the described work will be helpful to elucidate the functional genes and colonization mechanism of the dominant species.
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Skeletal development in the sea urchin relies upon protein families that contain intrinsic disorder, aggregation-prone, and conserved globular interactive domains. PLoS One 2019; 14:e0222068. [PMID: 31574084 PMCID: PMC6771980 DOI: 10.1371/journal.pone.0222068] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 08/21/2019] [Indexed: 12/02/2022] Open
Abstract
The formation of the sea urchin spicule skeleton requires the participation of hydrogel-forming protein families that regulate mineral nucleation and nanoparticle assembly processes that give rise to the spicule. However, the structure and molecular behavior of these proteins is not well established, and thus our ability to understand this process is hampered. We embarked on a study of sea urchin spicule proteins using a combination of biophysical and bioinformatics techniques. Our biophysical findings indicate that recombinant variants of the two most studied spicule matrix proteins, SpSM50 and SpSM30B/C (S. purpuratus) have a conformational landscape that include a C-terminal random coil/intrinsically disordered MAPQG sequence coupled to a conserved, folded N-terminal C-type lectin-like (CTLL) domain, with SpSM50 > SpSM30B/C with regard to intrinsic disorder. Both proteins possess solvent-accessible unfolded MAQPG sequence regions where Asn, Gln, and Arg residues may be accessible for protein hydrogel interactions with water molecules. Our bioinformatics study included seven other spicule matrix proteins where we note similarities between these proteins and rare, unusual proteins that possess folded and unfolded traits. Moreover, spicule matrix proteins possess three types of sequences: intrinsically disordered, amyloid-like, and folded protein-protein interactive. Collectively these reactive domains would be capable of driving protein assembly and hydrogel formation. Interestingly, three types of global conformations are predicted for the nine member protein set, wherein we note variations in the arrangement of intrinsically disordered and interactive globular domains. These variations may reflect species-specific requirements for spiculogenesis. We conclude that the molecular landscape of spicule matrix protein families enables them to function as hydrogelators, nucleators, and assemblers of mineral nanoparticles.
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Shimizu K, Kimura K, Isowa Y, Oshima K, Ishikawa M, Kagi H, Kito K, Hattori M, Chiba S, Endo K. Insights into the Evolution of Shells and Love Darts of Land Snails Revealed from Their Matrix Proteins. Genome Biol Evol 2019; 11:380-397. [PMID: 30388206 PMCID: PMC6368272 DOI: 10.1093/gbe/evy242] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/31/2018] [Indexed: 12/14/2022] Open
Abstract
Over the past decade, many skeletal matrix proteins that are possibly related to calcification have been reported in various calcifying animals. Molluscs are among the most diverse calcifying animals and some gastropods have adapted to terrestrial ecological niches. Although many shell matrix proteins (SMPs) have already been reported in molluscs, most reports have focused on marine molluscs, and the SMPs of terrestrial snails remain unclear. In addition, some terrestrial stylommatophoran snails have evolved an additional unique calcified character, called a “love dart,” used for mating behavior. We identified 54 SMPs in the terrestrial snail Euhadra quaesita, and found that they contain specific domains that are widely conserved in molluscan SMPs. However, our results also suggest that some of them possibly have evolved independently by domain shuffling, domain recruitment, or gene co-option. We then identified four dart matrix proteins, and found that two of them are the same proteins as those identified as SMPs. Our results suggest that some dart matrix proteins possibly have evolved by independent gene co-option from SMPs during dart evolution events. These results provide a new perspective on the evolution of SMPs and “love darts” in land snails.
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Affiliation(s)
- Keisuke Shimizu
- Department of Earth and Planetary Science, The University of Tokyo, Hongo, Japan.,College of Life and Environmental Sciences, University of Exeter, United Kingdom
| | - Kazuki Kimura
- Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan.,Research Institute for Ulleungdo and Dokdo Islands, Kyungpook National University, Bukgu, Daegu, Korea
| | - Yukinobu Isowa
- Organization for the Strategic Coordination of Research and Intellectual Properties, Meiji University, Kawasaki, Kanagawa, Japan
| | - Kenshiro Oshima
- Center for Omics and Bioinformatics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Makiko Ishikawa
- Department of Earth and Planetary Science, The University of Tokyo, Hongo, Japan.,Faculty of Animal Health Technology, Yamazaki University of Animal Health Technology, Hachioji, Tokyo, Japan
| | - Hiroyuki Kagi
- Geochemical Research Center, Graduate School of Science, The University of Tokyo, Hongo, Japan
| | - Keiji Kito
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Kanagawa, Japan
| | - Masahira Hattori
- Center for Omics and Bioinformatics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan.,Cooperative Major of Advanced Health Science, Graduate School of Advanced Science and Engineering, Waseda University, Japan
| | - Satoshi Chiba
- Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan
| | - Kazuyoshi Endo
- Department of Earth and Planetary Science, The University of Tokyo, Hongo, Japan
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4
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Kocot KM, Aguilera F, McDougall C, Jackson DJ, Degnan BM. Sea shell diversity and rapidly evolving secretomes: insights into the evolution of biomineralization. Front Zool 2016; 13:23. [PMID: 27279892 PMCID: PMC4897951 DOI: 10.1186/s12983-016-0155-z] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 05/27/2016] [Indexed: 12/21/2022] Open
Abstract
An external skeleton is an essential part of the body plan of many animals and is thought to be one of the key factors that enabled the great expansion in animal diversity and disparity during the Cambrian explosion. Molluscs are considered ideal to study the evolution of biomineralization because of their diversity of highly complex, robust and patterned shells. The molluscan shell forms externally at the interface of animal and environment, and involves controlled deposition of calcium carbonate within a framework of macromolecules that are secreted from the dorsal mantle epithelium. Despite its deep conservation within Mollusca, the mantle is capable of producing an incredible diversity of shell patterns, and macro- and micro-architectures. Here we review recent developments within the field of molluscan biomineralization, focusing on the genes expressed in the mantle that encode secreted proteins. The so-called mantle secretome appears to regulate shell deposition and patterning and in some cases becomes part of the shell matrix. Recent transcriptomic and proteomic studies have revealed marked differences in the mantle secretomes of even closely-related molluscs; these typically exceed expected differences based on characteristics of the external shell. All mantle secretomes surveyed to date include novel genes encoding lineage-restricted proteins and unique combinations of co-opted ancient genes. A surprisingly large proportion of both ancient and novel secreted proteins containing simple repetitive motifs or domains that are often modular in construction. These repetitive low complexity domains (RLCDs) appear to further promote the evolvability of the mantle secretome, resulting in domain shuffling, expansion and loss. RLCD families further evolve via slippage and other mechanisms associated with repetitive sequences. As analogous types of secreted proteins are expressed in biomineralizing tissues in other animals, insights into the evolution of the genes underlying molluscan shell formation may be applied more broadly to understanding the evolution of metazoan biomineralization.
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Affiliation(s)
- Kevin M Kocot
- School of Biological Sciences, University of Queensland, Brisbane, Queensland 4072 Australia.,Current address: Department of Biological Sciences and Alabama Museum of Natural History, The University of Alabama, Tuscaloosa, Alabama 35487 USA
| | - Felipe Aguilera
- School of Biological Sciences, University of Queensland, Brisbane, Queensland 4072 Australia.,Current address: Sars International Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgate 55, Bergen, 5008 Norway
| | - Carmel McDougall
- School of Biological Sciences, University of Queensland, Brisbane, Queensland 4072 Australia
| | - Daniel J Jackson
- Department of Geobiology, Goldschmidtstr.3, Georg-August University of Göttingen, 37077 Göttingen, Germany
| | - Bernard M Degnan
- School of Biological Sciences, University of Queensland, Brisbane, Queensland 4072 Australia
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5
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Karakostis K, Zanella-Cléon I, Immel F, Guichard N, Dru P, Lepage T, Plasseraud L, Matranga V, Marin F. A minimal molecular toolkit for mineral deposition? Biochemistry and proteomics of the test matrix of adult specimens of the sea urchin Paracentrotus lividus. J Proteomics 2016; 136:133-44. [DOI: 10.1016/j.jprot.2016.01.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 12/22/2015] [Accepted: 01/04/2016] [Indexed: 12/16/2022]
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6
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Mao Y, Satchell PG, Luan X, Diekwisch TGH. SM50 repeat-polypeptides self-assemble into discrete matrix subunits and promote appositional calcium carbonate crystal growth during sea urchin tooth biomineralization. Ann Anat 2015; 203:38-46. [PMID: 26194158 DOI: 10.1016/j.aanat.2015.06.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 06/21/2015] [Accepted: 06/22/2015] [Indexed: 10/23/2022]
Abstract
The two major proteins involved in vertebrate enamel formation and echinoderm sea urchin tooth biomineralization, amelogenin and SM50, are both characterized by elongated polyproline repeat domains in the center of the macromolecule. To determine the role of polyproline repeat polypeptides in basal deuterostome biomineralization, we have mapped the localization of SM50 as it relates to crystal growth, conducted self-assembly studies of SM50 repeat polypeptides, and examined their effect on calcium carbonate and apatite crystal growth. Electron micrographs of the growth zone of Strongylocentrotus purpuratus sea urchin teeth documented a series of successive events from intravesicular mineral nucleation to mineral deposition at the interface between tooth surface and odontoblast syncytium. Using immunohistochemistry, SM50 was detected within the cytoplasm of cells associated with the developing tooth mineral, at the mineral secreting front, and adjacent to initial mineral deposits, but not in muscles and ligaments. Polypeptides derived from the SM50 polyproline alternating hexa- and hepta-peptide repeat region (SM50P6P7) formed highly discrete, donut-shaped self-assembly patterns. In calcium carbonate crystal growth studies, SM50P6P7 repeat peptides triggered the growth of expansive networks of fused calcium carbonate crystals while in apatite growth studies, SM50P6P7 peptides facilitated the growth of needle-shaped and parallel arranged crystals resembling those found in developing vertebrate enamel. In comparison, SM50P6P7 surpassed the PXX24 polypeptide repeat region derived from the vertebrate enamel protein amelogenin in its ability to promote crystal nucleation and appositional crystal growth. Together, these studies establish the SM50P6P7 polyproline repeat region as a potent regulator in the protein-guided appositional crystal growth that occurs during continuous tooth mineralization and eruption. In addition, our studies highlight the role of species-specific polyproline repeat motifs in the formation of discrete self-assembled matrices and the resulting control of mineral growth.
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Affiliation(s)
- Yelin Mao
- UIC College of Dentistry, Department of Orthodontics, USA
| | | | - Xianghong Luan
- UIC College of Dentistry, Department of Orthodontics, USA; UIC College of Dentistry, Department of Oral Biology, USA
| | - Thomas G H Diekwisch
- UIC College of Dentistry, Department of Oral Biology, USA; Baylor College of Dentistry, Department of Periodontics, USA.
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Yazici H, Fong H, Wilson B, Oren E, Amos F, Zhang H, Evans J, Snead M, Sarikaya M, Tamerler C. Biological response on a titanium implant-grade surface functionalized with modular peptides. Acta Biomater 2013; 9:5341-52. [PMID: 23159566 DOI: 10.1016/j.actbio.2012.11.004] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Revised: 10/18/2012] [Accepted: 11/02/2012] [Indexed: 12/21/2022]
Abstract
Titanium (Ti) and its alloys are among the most successful implantable materials for dental and orthopedic applications. The combination of excellent mechanical and corrosion resistance properties makes them highly desirable as endosseous implants that can withstand a demanding biomechanical environment. Yet, the success of the implant depends on its osteointegration, which is modulated by the biological reactions occurring at the interface of the implant. A recent development for improving biological responses on the Ti-implant surface has been the realization that bifunctional peptides can impart material binding specificity not only because of their molecular recognition of the inorganic material surface, but also through their self-assembly and ease of biological conjugation properties. To assess peptide-based functionalization on bioactivity, the present authors generated a set of peptides for implant-grade Ti, using cell surface display methods. Out of 60 unique peptides selected by this method, two of the strongest titanium binding peptides, TiBP1 and TiBP2, were further characterized for molecular structure and adsorption properties. These two peptides demonstrated unique, but similar molecular conformations different from that of a weak binder peptide, TiBP60. Adsorption measurements on a Ti surface revealed that their disassociation constants were 15-fold less than TiBP60. Their flexible and modular use in biological surface functionalization were demonstrated by conjugating them with an integrin recognizing peptide motif, RGDS. The functionalization of the Ti surface by the selected peptides significantly enhanced the bioactivity of osteoblast and fibroblast cells on implant-grade materials.
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8
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So CR, Kulp JL, Oren EE, Zareie H, Tamerler C, Evans JS, Sarikaya M. Molecular recognition and supramolecular self-assembly of a genetically engineered gold binding peptide on Au{111}. ACS NANO 2009; 3:1525-1531. [PMID: 19438257 DOI: 10.1021/nn900171s] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The understanding of biomineralization and realization of biology-inspired materials technologies depends on understanding the nature of the chemical and physical interactions between proteins and biominerals or synthetically made inorganic materials. Recently, combinatorial genetic techniques permit the isolation of peptides recognizing specific inorganic materials that are used as molecular building blocks for novel applications. Little is known about the molecular structure of these peptides and the specific recognition mechanisms onto their counterpart inorganic surfaces. Here, we report high-resolution atomic force microscopy (AFM), molecular simulation (MS), and geometrical docking studies that detail the formation of an ordered supramolecular self-assembly of a genetically engineered gold binding peptide, 3rGBP(1) ([MHGKTQATSGTIQS](3)), correlating with the symmetry of the Au{111} surface lattice. Using simulated annealing molecular dynamics (SA/MD) studies based on nuclear magnetic resonance (NMR), we confirmed the intrinsic disorder of 3rGBP(1) and identified putative Au docking sites where surface-exposed side chains align with both the <110> and <211> Miller indices of the Au lattice. Our results provide fundamental insight for an atomistic understanding of peptide/solid interfaces and the intrinsic disorder that is inherent in some of these peptide sequences. Analogous to the well-established atomically controlled thin-film heterostructure formation on semiconductor substrates, the basis of today's microelectronics, the fundamental observations of peptide-solid interactions here may well form the basis of peptide-based hybrid molecular technologies of the future.
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Affiliation(s)
- Christopher R So
- Genetically Engineered Materials Science and Engineering Center, Department of Materials Science and Engineering, University of Washington, Seattle, WA 98105, USA
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9
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Delak K, Harcup C, Lakshminarayanan R, Sun Z, Fan Y, Moradian-Oldak J, Evans JS. The tooth enamel protein, porcine amelogenin, is an intrinsically disordered protein with an extended molecular configuration in the monomeric form. Biochemistry 2009; 48:2272-81. [PMID: 19236004 PMCID: PMC2748245 DOI: 10.1021/bi802175a] [Citation(s) in RCA: 125] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Amelogenins make up a class of proteins associated with the formation of mineralized enamel in vertebrates, possess highly conserved N- and C-terminal sequence regions, and represent an interesting model protein system for understanding biomineralization and protein assembly. Using bioinformatics, we report here the identification of molecular traits that classify 12 amelogenin proteins as members of the intrinsically disordered or unstructured protein family (IDPs), a group of proteins that normally exist as unfolded species but are capable of transformation to a folded state as part of their overall function. Using biophysical techniques (CD and NMR), we follow up on our bioinformatics studies and confirm that one of the amelogenins, recombinant porcine rP172, exists in an extended, unfolded state in the monomeric form. This protein exhibits evidence of conformational exchange between two states, and this exchange may be mediated by Pro residues in the sequence. Although the protein is globally unfolded, we detect the presence of local residual secondary structure [alpha-helix, extended beta-strand, turn/loop, and polyproline type II (PPII)] that may serve several functional roles within the enamel matrix. The extended, labile conformation of rP172 amelogenin is compatible with the known functions of amelogenin in enamel biomineralization, i.e., self-assembly, associations with other enamel matrix proteins and with calcium phosphate biominerals, and interaction with cell receptors. It is likely that the labile structure of this protein facilitates interactions of amelogenin with other macromolecules or with minerals for achievement of internal protein stabilization.
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Affiliation(s)
- Katya Delak
- Laboratory for Chemical Physics, New York University, 345 East 24th Street, Room 1007, New York, New York 10010
| | - Craig Harcup
- Laboratory for Chemical Physics, New York University, 345 East 24th Street, Room 1007, New York, New York 10010
| | - Rajamani Lakshminarayanan
- Center for Craniofacial Biology, CSA 107, School of Dentistry, Health Sciences Center, University of Southern California, Los Angeles, California 90033
| | - Zhi Sun
- Center for Craniofacial Biology, CSA 107, School of Dentistry, Health Sciences Center, University of Southern California, Los Angeles, California 90033
| | - Yuwwei Fan
- Center for Craniofacial Biology, CSA 107, School of Dentistry, Health Sciences Center, University of Southern California, Los Angeles, California 90033
| | - Janet Moradian-Oldak
- Center for Craniofacial Biology, CSA 107, School of Dentistry, Health Sciences Center, University of Southern California, Los Angeles, California 90033
| | - John Spencer Evans
- Laboratory for Chemical Physics, New York University, 345 East 24th Street, Room 1007, New York, New York 10010
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10
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Mann K, Poustka AJ, Mann M. In-depth, high-accuracy proteomics of sea urchin tooth organic matrix. Proteome Sci 2008; 6:33. [PMID: 19068105 PMCID: PMC2614417 DOI: 10.1186/1477-5956-6-33] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2008] [Accepted: 12/09/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The organic matrix contained in biominerals plays an important role in regulating mineralization and in determining biomineral properties. However, most components of biomineral matrices remain unknown at present. In sea urchin tooth, which is an important model for developmental biology and biomineralization, only few matrix components have been identified. The recent publication of the Strongylocentrotus purpuratus genome sequence rendered possible not only the identification of genes potentially coding for matrix proteins, but also the direct identification of proteins contained in matrices of skeletal elements by in-depth, high-accuracy proteomic analysis. RESULTS We identified 138 proteins in the matrix of tooth powder. Only 56 of these proteins were previously identified in the matrices of test (shell) and spine. Among the novel components was an interesting group of five proteins containing alanine- and proline-rich neutral or basic motifs separated by acidic glycine-rich motifs. In addition, four of the five proteins contained either one or two predicted Kazal protease inhibitor domains. The major components of tooth matrix were however largely identical to the set of spicule matrix proteins and MSP130-related proteins identified in test (shell) and spine matrix. Comparison of the matrices of crushed teeth to intact teeth revealed a marked dilution of known intracrystalline matrix proteins and a concomitant increase in some intracellular proteins. CONCLUSION This report presents the most comprehensive list of sea urchin tooth matrix proteins available at present. The complex mixture of proteins identified may reflect many different aspects of the mineralization process. A comparison between intact tooth matrix, presumably containing odontoblast remnants, and crushed tooth matrix served to differentiate between matrix components and possible contributions of cellular remnants. Because LC-MS/MS-based methods directly measures peptides our results validate many predicted genes and confirm the existence of the corresponding proteins. Knowledge of the components of this model system may stimulate further experiments aiming at the elucidation of structure, function, and interaction of biomineral matrix components.
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Affiliation(s)
- Karlheinz Mann
- Max-Planck-Institut für Biochemie, Abteilung Proteomics und Signaltransduktion, Martinsried, Germany.
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11
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Evans JS. “Tuning in” to Mollusk Shell Nacre- and Prismatic-Associated Protein Terminal Sequences. Implications for Biomineralization and the Construction of High Performance Inorganic−Organic Composites. Chem Rev 2008; 108:4455-62. [DOI: 10.1021/cr078251e] [Citation(s) in RCA: 137] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- John Spencer Evans
- Laboratory for Chemical Physics, Center for Biomolecular Materials Spectroscopy, New York University, 345 E. 24th Street, Room 1007, New York, New York, 10010
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12
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Collino S, Kim IW, Evans JS. Identification and structural characterization of an unusual RING-like sequence within an extracellular biomineralization protein, AP7. Biochemistry 2008; 47:3745-55. [PMID: 18298090 DOI: 10.1021/bi701949p] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The RING or Really Interesting New Gene represents a family of eukaryotic sequences that bind Zn (II) ions and participate in intracellular processes involving protein-protein interaction. Although found in over 400 different proteins, very little is known regarding the structure-function properties of these domains because of the aggregation problems associated with RING sequences. To augment this data set, we report an unusual 36 AA C-terminal sequence of an extracellular matrix mollusk shell protein, AP7, that exhibits partial homology to the RING family. This Cys, His-containing sequence, termed AP7C, binds Zn (II) and other multivalent ions, but does not utilize a tetracoordinate complexation scheme for binding such as that found in Zn (II) finger polypeptides. Moreover, unlike Zn (II) finger and RING domains, this 36 AA can fold into a relatively stable structure in the absence of Zn (II). This folded structure consists of three short helical segments (A, B, and C), with segments A and B separated by a 4 AA type I beta-turn region and segments B and C separated by a 7 AA loop-like region. Interestingly, the putative RING-like region, -RRPFHECALCYSI-, experiences slow conformational exchange between two structural states in solution, most likely in response to imido ring interconversion at P8 and P21. Poisson-Boltzmann solvation calculations reveal that the AP7C molecular surface possesses a cationic region near its N-terminus, which lies adjacent to the 30 AA mineral modification domain in the AP7 protein. Given that the AP7C sequence does not influence mineralization, it is probable that this cationic pseudo-RING region is utilized by the AP7 protein for other tasks such as protein-protein interaction within the mollusk shell matrix.
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Affiliation(s)
- Sebastiano Collino
- Laboratory for Chemical Physics, Center for Biomolecular Materials Spectroscopy, New York University, 345 E. 24th Street, Room 1007, New York, New York 10010, USA
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13
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Jackson DJ, Wörheide G, Degnan BM. Dynamic expression of ancient and novel molluscan shell genes during ecological transitions. BMC Evol Biol 2007; 7:160. [PMID: 17845714 PMCID: PMC2034539 DOI: 10.1186/1471-2148-7-160] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2006] [Accepted: 09/10/2007] [Indexed: 11/17/2022] Open
Abstract
Background The Mollusca constitute one of the most morphologically and ecologically diverse metazoan phyla, occupying a wide range of marine, terrestrial and freshwater habitats. The evolutionary success of the molluscs can in part be attributed to the evolvability of the external shell. Typically, the shell first forms during embryonic and larval development, changing dramatically in shape, colour and mineralogical composition as development and maturation proceeds. Major developmental transitions in shell morphology often correlate with ecological transitions (e.g. from a planktonic to benthic existence at metamorphosis). While the genes involved in molluscan biomineralisation are beginning to be identified, there is little understanding of how these are developmentally regulated, or if the same genes are operational at different stages of the mollusc's life. Results Here we relate the developmental expression of nine genes in the tissue responsible for shell production – the mantle – to ecological transitions that occur during the lifetime of the tropical abalone Haliotis asinina (Vetigastropoda). Four of these genes encode evolutionarily ancient proteins, while four others encode secreted proteins with little or no identity to known proteins. Another gene has been previously described from the mantle of another haliotid vetigastropod. All nine genes display dynamic spatial and temporal expression profiles within the larval shell field and juvenile mantle. Conclusion These expression data reflect the regulatory complexity that underlies molluscan shell construction from larval stages to adulthood, and serves to highlight the different ecological demands placed on each stage. The use of both ancient and novel genes in all stages of shell construction also suggest that a core set of shell-making genes was provided by a shared metazoan ancestor, which has been elaborated upon to produce the range of molluscan shell types we see today.
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Affiliation(s)
- Daniel J Jackson
- School of Integrative Biology, University of Queensland, Brisbane Queensland 4072, Australia
- Department of Geobiology, Geoscience Centre, University of Göttingen, Goldschmidtstr.3, 37077, Göttingen, Germany
| | - Gert Wörheide
- Department of Geobiology, Geoscience Centre, University of Göttingen, Goldschmidtstr.3, 37077, Göttingen, Germany
| | - Bernard M Degnan
- School of Integrative Biology, University of Queensland, Brisbane Queensland 4072, Australia
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Quinn P, Bowers RM, Zhang X, Wahlund TM, Fanelli MA, Olszova D, Read BA. cDNA microarrays as a tool for identification of biomineralization proteins in the coccolithophorid Emiliania huxleyi (Haptophyta). Appl Environ Microbiol 2006; 72:5512-26. [PMID: 16885305 PMCID: PMC1538752 DOI: 10.1128/aem.00343-06] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Marine unicellular coccolithophore algae produce species-specific calcite scales otherwise known as coccoliths. While the coccoliths and their elaborate architecture have attracted the attention of investigators from various scientific disciplines, our knowledge of the underpinnings of the process of biomineralization in this alga is still in its infancy. The processes of calcification and coccolithogenesis are highly regulated and likely to be complex, requiring coordinated expression of many genes and pathways. In this study, we have employed cDNA microarrays to investigate changes in gene expression associated with biomineralization in the most abundant coccolithophorid, Emiliania huxleyi. Expression profiling of cultures grown under calcifying and noncalcifying conditions has been carried out using cDNA microarrays corresponding to approximately 2,300 expressed sequence tags. A total of 127 significantly up- or down-regulated transcripts were identified using a P value of 0.01 and a change of >2.0-fold. Real-time reverse transcriptase PCR was used to test the overall validity of the microarray data, as well as the relevance of many of the proteins predicted to be associated with biomineralization, including a novel gamma-class carbonic anhydrase (A. R. Soto, H. Zheng, D. Shoemaker, J. Rodriguez, B. A. Read, and T. M. Wahlund, Appl. Environ. Microbiol. 72:5500-5511, 2006). Differentially regulated genes include those related to cellular metabolism, ion channels, transport proteins, vesicular trafficking, and cell signaling. The putative function of the vast majority of candidate transcripts could not be defined. Nonetheless, the data described herein represent profiles of the transcription changes associated with biomineralization-related pathways in E. huxleyi and have identified novel and potentially useful targets for more detailed analysis.
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Affiliation(s)
- Patrick Quinn
- Department of Biological Sciences, California State University-San Marcos, San Marcos, CA 92078, USA
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Nguyen B, Bowers RM, Wahlund TM, Read BA. Suppressive subtractive hybridization of and differences in gene expression content of calcifying and noncalcifying cultures of Emiliania huxleyi strain 1516. Appl Environ Microbiol 2005; 71:2564-75. [PMID: 15870347 PMCID: PMC1087533 DOI: 10.1128/aem.71.5.2564-2575.2005] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The marine coccolithophorid Emiliania huxleyi is a cosmopolitan alga intensely studied in relation to global carbon cycling, biogeochemistry, marine ecology, and biomineralization processes. The biomineralization capabilities of coccolithophorids have attracted the attention of scientists interested in exploiting this ability for the development of materials science and biomedical and biotechnological applications. Although it has been well documented that biomineralization in E. huxleyi is promoted by growth under phosphate-limited conditions, the genes and proteins that govern the processes of calcification and coccolithogenesis remain unknown. Suppressive subtractive hybridization (SSH) libraries were constructed from cultures grown in phosphate-limited and phosphate-replete media as tester and driver populations for reciprocal SSH procedures. Positive clones from each of the two libraries were randomly selected, and dot blotting was performed for the analysis of expression patterns. A total of 513 clones from the phosphate-replete library and 423 clones from the phosphate-limited library were sequenced, assembled, and compared to sequences in GenBank using BLASTX. Of the 103 differentially expressed gene fragments from the phosphate-replete library, 34% showed significant homology to other known proteins, while only 23% of the 65 differentially expressed gene fragments from the phosphate-limited library showed homology to other proteins. To further assess mRNA expression, real-time RT-PCR analysis was employed and expression profiles were generated over a 14-day time course for three clones from the phosphate-replete library and five clones from the phosphate-limited library. The fragments isolated provide the basis for future cloning of full-length genes and functional analysis.
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Affiliation(s)
- Binh Nguyen
- Department of Biological Sciences, California State University, San Marcos, CA 92096-0001, USA
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Wustman BA, Morse DE, Evans JS. Structural characterization of the N-terminal mineral modification domains from the molluscan crystal-modulating biomineralization proteins, AP7 and AP24. Biopolymers 2004; 74:363-76. [PMID: 15222016 DOI: 10.1002/bip.20086] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The AP7 and AP24 proteins represent a class of mineral-interaction polypeptides that are found in the aragonite-containing nacre layer of mollusk shell (H. rufescens). These proteins have been shown to preferentially interfere with calcium carbonate mineral growth in vitro. It is believed that both proteins play an important role in aragonite polymorph selection in the mollusk shell. Previously, we demonstrated the 1-30 amino acid (AA) N-terminal sequences of AP7 and AP24 represent mineral interaction/modification domains in both proteins, as evidenced by their ability to frustrate calcium carbonate crystal growth at step edge regions. In this present report, using free N-terminal, C(alpha)-amide "capped" synthetic polypeptides representing the 1-30 AA regions of AP7 (AP7-1 polypeptide) and AP24 (AP24-1 polypeptide) and NMR spectroscopy, we confirm that both N-terminal sequences possess putative Ca (II) interaction polyanionic sequence regions (2 x -DD- in AP7-1, -DDDED- in AP24-1) that are random coil-like in structure. However, with regard to the remaining sequences regions, each polypeptide features unique structural differences. AP7-1 possesses an extended beta-strand or polyproline type II-like structure within the A11-M10, S12-V13, and S28-I27 sequence regions, with the remaining sequence regions adopting a random-coil-like structure, a trait common to other polyelectrolyte mineral-associated polypeptide sequences. Conversely, AP24-1 possesses random coil-like structure within A1-S9 and Q14-N16 sequence regions, and evidence for turn-like, bend, or loop conformation within the G10-N13, Q17-N24, and M29-F30 sequence regions, similar to the structures identified within the putative elastomeric proteins Lustrin A and sea urchin spicule matrix proteins. The similarities and differences in AP7 and AP24 N-terminal domain structure are discussed with regard to joint AP7-AP24 protein modification of calcium carbonate growth.
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Affiliation(s)
- Brandon A Wustman
- Laboratory for Chemical Physics, New York University, 345 E. 24th Street, New York, NY 10010, USA
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Caubet C, Jonca N, Lopez F, Estève JP, Simon M, Serre G. Homo-oligomerization of human corneodesmosin is mediated by its N-terminal glycine loop domain. J Invest Dermatol 2004; 122:747-54. [PMID: 15086562 DOI: 10.1111/j.0022-202x.2004.22331.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Corneodesmosin (CDSN), a glycoprotein expressed during the late stages of epidermal differentiation, localizes in the extracellular core of upper desmosomes and of corneodesmosomes. Since it displays homophilic adhesive properties, CDSN is thought to reinforce cell-cell cohesion within the upper layers of the epidermis. CDSN presents two serine- and glycine-rich domains in its N- and C-terminus that may fold into highly flexible and adhesive secondary structures called glycine loops. We analyzed the importance of these domains in CDSN homophilic adhesion by producing full-length and truncated recombinant forms of the protein deleted of the N- and/or the C-terminal domain. The adhesive properties of the various proteins were then tested in vitro by overlay binding assays and surface plasmon resonance quantitative analysis. Experiments evidenced the homophilic adhesive properties of the N-terminal glycine loop domain, confirming its involvement in CDSN-CDSN interactions. They further indicated that most of the C-terminal domain is not necessary for the adhesive properties of the protein. The dissociation constant (K(D)) was calculated to be 1.3x10(-5) M. This interaction strength might allow dynamic regulation of the CDSN-CDSN association to occur in vivo. Moreover, molecular filtration analyses demonstrated for the first time that non-glycosylated CDSN is able to spontaneously form large homo-oligomers in vitro and that the N-terminal glycine loop domain is necessary for the formation of these macromolecular complexes.
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Affiliation(s)
- Cécile Caubet
- UMR 5165 Epidermis Differentiation and Rheumatoid Autoimmunity CNRS, University of Toulouse III, Institut Fédératif de Recherche Claude de Préval, IFR30 (INSERM-CNRS Université Paul Sabatier-Centre Hospitalier Universitaire), Toulouse, France
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Ajikumar PK, Lakshminarayanan R, Ong BT, Valiyaveettil S, Kini RM. Eggshell matrix protein mimics: designer peptides to induce the nucleation of calcite crystal aggregates in solution. Biomacromolecules 2003; 4:1321-6. [PMID: 12959601 DOI: 10.1021/bm034101b] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ansocalcin is a novel goose eggshell matrix protein with 132 amino acid residues, which induces the formation of polycrystalline calcite aggregates in in vitro crystallization experiments. The central region of ansocalcin is characterized by the presence of multiplets of charged amino acids. To investigate the specific role of charged amino acid multiplets in the crystal nucleation, three short peptides REWD-16, REWDP-17 (containing charged doublets), and RADA-16 (alternating charged residues) were synthesized and characterized. The aggregation of these peptides in solution was investigated using circular dichroism, intrinsic tryptophan fluorescence, and dynamic light scattering experiments. The peptides REWD-16 and REWDP-17 induced the polycrystalline calcite crystal aggregates, whereas RADA-16 did not induce significant changes in calcite crystal morphology or aggregate formation in in vitro crystallization experiments. The lattice and morphology of the calcite crystals were characterized using X-ray diffraction and scanning electron microscope. The results discussed in this paper reveal the importance of multiplets of charged amino acid residues toward the nucleation of polycrystalline calcite crystal aggregates in solution.
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Affiliation(s)
- Parayil Kumaran Ajikumar
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore
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Abstract
Most metazoans require skeletal support systems. While the formation of bones and teeth in vertebrates has been well studied, endo- and exoskeleton development of non-vertebrates, especially calcification during terminal differentiation, has been neglected. Biomineralization of skeletons in invertebrates presents interesting research opportunities. We undertake here to survey some of the better understood examples of skeletal development in selected invertebrates. The differentiation of the skeletal spicules of euechinoid larvae and other non-vertebrate deuterostomes, the shells of molluscs, and the calcification of crustacean carapaces are surveyed. The diversity of these different kinds of animals and our present limited understanding make it difficult to identify unifying themes, but there certainly are unifying questions: How is the mineral precursor secreted? What is the nature of the interaction of mineral with the matrix proteins of the skeleton? Is there any conservation of protein domains in matrix proteins found in skeletal elements from different phyla? Are there common strategies in the development of organs that form mineralized structures?
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Affiliation(s)
- Fred H Wilt
- Department of Molecular and Cell Biology, University of California, Berkeley, 142 Life Sciences Addition, Berkeley, California 94720-3200, USA.
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Evans JS. ‘Apples’ and ‘oranges’: comparing the structural aspects of biomineral- and ice-interaction proteins. Curr Opin Colloid Interface Sci 2003. [DOI: 10.1016/s1359-0294(03)00009-8] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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