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Glycoproteins Involved in Sea Urchin Temporary Adhesion. Mar Drugs 2023; 21:md21030145. [PMID: 36976195 PMCID: PMC10057474 DOI: 10.3390/md21030145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 02/10/2023] [Accepted: 02/18/2023] [Indexed: 03/03/2023] Open
Abstract
Biomedical adhesives, despite having been used increasingly in recent years, still face a major technological challenge: strong adhesion in wet environments. In this context, biological adhesives secreted by marine invertebrates have appealing characteristics to incorporate into new underwater biomimetic adhesives: water resistance, nontoxicity and biodegradability. Little is still known about temporary adhesion. Recently, a transcriptomic differential analysis of sea urchin Paracentrotus lividus tube feet pinpointed 16 adhesive/cohesive protein candidates. In addition, it has been demonstrated that the adhesive secreted by this species is composed of high molecular weight proteins associated with N-Acetylglucosamine in a specific chitobiose arrangement. As a follow-up, we aimed to investigate which of these adhesive/cohesive protein candidates were glycosylated through lectin pulldowns, protein identification by mass spectroscopy and in silico characterization. We demonstrate that at least five of the previously identified protein adhesive/cohesive candidates are glycoproteins. We also report the involvement of a third Nectin variant, the first adhesion-related protein to be identified in P. lividus. By providing a deeper characterization of these adhesive/cohesive glycoproteins, this work advances our understanding of the key features that should be replicated in future sea urchin-inspired bioadhesives.
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2
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Anand PP, Shibu Vardhanan Y. Molecular cloning, expression, mRNA secondary structure and immunological characterization of mussel foot proteins (Mfps) (Mollusca: Bivalvia). J Biomol Struct Dyn 2023; 41:12242-12266. [PMID: 36688334 DOI: 10.1080/07391102.2023.2166996] [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] [Received: 09/12/2022] [Accepted: 01/01/2023] [Indexed: 01/24/2023]
Abstract
The macroscale production of mussel foot proteins (Mfps) in the expression system has not succeeded to date. The principal reasons for this are low levels of expression and yield of Mfps, lack of post-translational modifications (PTMs), and immunological toxic effects on the host system. Identification of post-translational modification sites, suitable expression hosts, and immunological responses through an experimental approach is very costly and time-consuming. However, in the present study, in silico post-translation modification, antigenicity, allergenicity, and the immunological reaction of all available Mfps were characterized. Furthermore, all Mfps were codon optimized in three different expression systems to determine the best expression host. Finally, we performed the in-silico cloning of all codon-optimized Mfps in a suitable host (E. coli K12, pET28a(+) vector) and analyzed the secondary structure of mRNA and its structural stability. Among the 78 Mfps, six fps are considered potential allergenic proteins, six fps are considered non-allergenic proteins, and all other fps are probably allergenic. High antigenicity was observed in bacterial cells as compared to yeast and tumor cells. Nevertheless, the predicted expression of Mfps in a bacterial host is higher than in other expression hosts. Important to note that all Mfps showed significant immunological activity in the human system, and we concluded that these antigenic, allergenic, and immunological properties are directly correlated with their amino acid composition. The study's major goal is to provide a comprehensive understanding of Mfps and aid in the future genetic engineering and expression of Mfps and its diverse applications in different fields.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- P P Anand
- Biochemistry & Toxicology Division, Department of Zoology, University of Calicut, Thenhipalam, Kerala, India
| | - Y Shibu Vardhanan
- Biochemistry & Toxicology Division, Department of Zoology, University of Calicut, Thenhipalam, Kerala, India
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3
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Sam S, Sung S, Krem S, Park S, Hwang DS, Kim D. Sum-Frequency Vibrational Spectroscopic Study of the Cation-π Interaction: Amine and Guanidine. J Phys Chem B 2022; 126:7621-7626. [PMID: 36166344 DOI: 10.1021/acs.jpcb.2c05709] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The cation-π interaction is an interaction between a positively charged cation and π electrons in an aromatic group of a molecule. It is considered to play key roles in signal transduction, stabilization of the protein structure, enzyme catalysis in biology, and wet adhesion and biomolecular condensation. In this study, octadecylguanidine hydrochloride (ODG) and octadecylamine (ODA) having guanidine and amine headgroups, respectively, are found to interact with π molecules (phenol or indole) as investigated by sum-frequency vibrational spectroscopy. ODG is unstable and does not form a neat monolayer on the water surface. However, after adding π molecules into subphase water, it becomes more stable against dissolution as evidenced by the appearance of its CHx peaks and a CH peak of the aromatic ring in the sum-frequency spectrum. Unlike ODG, ODA forms a stable monolayer on the water surface at a neutral pH. After adding π molecules into the solution, the amine-π interaction promotes the protonation of the amine headgroup and the penetration of the π molecules makes the ODA monolayer more disordered. Indole is found to be more effective in binding with the ODG as compared to phenol.
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Affiliation(s)
- Sokhuoy Sam
- Department of Physics, Sogang University, 35, Baekbeom-ro, Mapo-gu, Seoul 04107, Korea
| | - Siheon Sung
- Department of Physics, Sogang University, 35, Baekbeom-ro, Mapo-gu, Seoul 04107, Korea
| | - Sona Krem
- Department of Physics, Sogang University, 35, Baekbeom-ro, Mapo-gu, Seoul 04107, Korea
| | - Sohee Park
- Division of Environmental Science and Engineering (DESE), Pohang University of Science and Technology (POSTECH), 77 Cheongam-ro, Namgu, Pohang 37673, Korea
| | - Dong Soo Hwang
- Division of Environmental Science and Engineering (DESE), Pohang University of Science and Technology (POSTECH), 77 Cheongam-ro, Namgu, Pohang 37673, Korea
| | - Doseok Kim
- Department of Physics, Sogang University, 35, Baekbeom-ro, Mapo-gu, Seoul 04107, Korea
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Rouhová L, Sehadová H, Pauchová L, Hradilová M, Žurovcová M, Šerý M, Rindoš M, Žurovec M. Using the multi-omics approach to reveal the silk composition in Plectrocnemia conspersa. Front Mol Biosci 2022; 9:945239. [PMID: 36060257 PMCID: PMC9432349 DOI: 10.3389/fmolb.2022.945239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 07/19/2022] [Indexed: 11/29/2022] Open
Abstract
Similar to Lepidoptera, the larvae of Trichoptera are also capable of producing silk. Plectrocnemia conspersa, a predatory species belonging to the suborder Annulipalpia, builds massive silken retreats with preycapturing nets. In this study, we describe the silk glands of P. conspersa and use the multi-omics methods to obtain a complete picture of the fiber composition. A combination of silk gland-specific transcriptome and proteomic analyses of the spun-out fibers yielded 27 significant candidates whose full-length sequences and gene structures were retrieved from the publicly available genome database. About one-third of the candidates were completely novel proteins for which there are no described homologs, including a group of five pseudofibroins, proteins with a composition similar to fibroin heavy chain. The rest were homologs of lepidopteran silk proteins, although some had a larger number of paralogs. On the other hand, P. conspersa fibers lacked some proteins that are regular components in moth silk. In summary, the multi-omics approach provides an opportunity to compare the overall composition of silk with other insect species. A sufficient number of such studies will make it possible to distinguish between the basic components of all silks and the proteins that represent the adaptation of the fibers for specific purposes or environments.
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Affiliation(s)
- Lenka Rouhová
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Ceske Budejovice, Czechia
- Faculty of Science, University of South Bohemia, Ceske Budejovice, Czechia
| | - Hana Sehadová
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Ceske Budejovice, Czechia
- Faculty of Science, University of South Bohemia, Ceske Budejovice, Czechia
| | - Lucie Pauchová
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Ceske Budejovice, Czechia
| | - Miluše Hradilová
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Praha, Czechia
| | - Martina Žurovcová
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Ceske Budejovice, Czechia
| | - Michal Šerý
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Ceske Budejovice, Czechia
| | - Michal Rindoš
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Ceske Budejovice, Czechia
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Prague, Czechia
| | - Michal Žurovec
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Ceske Budejovice, Czechia
- Faculty of Science, University of South Bohemia, Ceske Budejovice, Czechia
- *Correspondence: Michal Žurovec,
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Lei Y, Guo K, Zhang Y, Zhang X, Qin L, Wang X, Zhu H, Guo Y, Yang W, Li B, Xia Q, Zhao P, Dong Z. Adhesive property and mechanism of silkworm egg glue protein. Acta Biomater 2021; 134:499-512. [PMID: 34311106 DOI: 10.1016/j.actbio.2021.07.039] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 07/01/2021] [Accepted: 07/20/2021] [Indexed: 12/12/2022]
Abstract
Egg glue proteins (EGPs) are produced by female insects, which can make the eggs firmly attached to the oviposition sites, not affected by wind and rain. Although EGPs are widespread in insects, they have been rarely characterized in molecular detail. Here, the full-length sequence and secondary structure of silkworm EGP is reported. A pentapeptide motif, G-G-N/K/D-Q/E/K-Q/P, was found to repeat 346 times, forming a hydrophilic and elastic β-spiral structure in the silkworm EGP. To reveal the adhesive property and mechanism, we extracted natural EGP from silkworm colleterial gland, and expressed recombinant EGP in Escherichia coli and Pichia pastoris. The glycosylated natural EGP and recombinant EGP from P. pastoris was found to have better adhesive strength than the non-glycosylated recombinant EGP from E. coli. In addition, two transglutaminases in the colleterial gland were found to contribute to the high adhesion of EGP by catalyzing the cross-linking. This study provides important insights into the structure-function relationships associated with this protein, thereby creating new opportunities for the use of insect EGP as a biomaterial. STATEMENT OF SIGNIFICANCE: Egg glue proteins are produced by female insects, which can make the eggs firmly attached to the oviposition sites, not affected by wind and rain. However, genes encoding insect egg glue proteins have not yet been reported, and the molecular mechanism underpinning their adhesion is still unknown. Our study makes a significant contribution to the literature as it identifies the sequence, structure, adhesive property, and mechanism of silkworm egg glue protein. Furthermore, it outlines key insights into the structure-function relationships associated with egg glue proteins. We believe that this paper will be of interest to the readership of your journal as it identifies the first complete sequence of insect egg glue proteins, thereby highlighting their potentials future applications in both the biomedical and technical fields.
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Minakata S, Manabe S, Inai Y, Ikezaki M, Nishitsuji K, Ito Y, Ihara Y. Protein C-Mannosylation and C-Mannosyl Tryptophan in Chemical Biology and Medicine. Molecules 2021; 26:molecules26175258. [PMID: 34500691 PMCID: PMC8433626 DOI: 10.3390/molecules26175258] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/25/2021] [Accepted: 08/26/2021] [Indexed: 12/25/2022] Open
Abstract
C-Mannosylation is a post-translational modification of proteins in the endoplasmic reticulum. Monomeric α-mannose is attached to specific Trp residues at the first Trp in the Trp-x-x-Trp/Cys (W-x-x-W/C) motif of substrate proteins, by the action of C-mannosyltransferases, DPY19-related gene products. The acceptor substrate proteins are included in the thrombospondin type I repeat (TSR) superfamily, cytokine receptor type I family, and others. Previous studies demonstrated that C-mannosylation plays critical roles in the folding, sorting, and/or secretion of substrate proteins. A C-mannosylation-defective gene mutation was identified in humans as the disease-associated variant affecting a C-mannosylation motif of W-x-x-W of ADAMTSL1, which suggests the involvement of defects in protein C-mannosylation in human diseases such as developmental glaucoma, myopia, and/or retinal defects. On the other hand, monomeric C-mannosyl Trp (C-Man-Trp), a deduced degradation product of C-mannosylated proteins, occurs in cells and extracellular fluids. Several studies showed that the level of C-Man-Trp is upregulated in blood of patients with renal dysfunction, suggesting that the metabolism of C-Man-Trp may be involved in human kidney diseases. Together, protein C-mannosylation is considered to play important roles in the biosynthesis and functions of substrate proteins, and the altered regulation of protein C-manosylation may be involved in the pathophysiology of human diseases. In this review, we consider the biochemical and biomedical knowledge of protein C-mannosylation and C-Man-Trp, and introduce recent studies concerning their significance in biology and medicine.
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Affiliation(s)
- Shiho Minakata
- Department of Biochemistry, Wakayama Medical University, 811-1 Kimiidera, Wakayama, Wakayama 641-0012, Japan; (S.M.); (Y.I.); (M.I.); (K.N.)
| | - Shino Manabe
- Pharmaceutical Department, The Institute of Medicinal Chemistry, Hoshi University, 2-4-41 Ebara, Shinagawa, Tokyo 142-8501, Japan;
- Research Center for Pharmaceutical Development, Graduate School of Pharmaceutical Science & Faculty of Pharmaceutical Sciences, Tohoku University, 6-3 Aoba, Sendai, Miyagi 980-8578, Japan
| | - Yoko Inai
- Department of Biochemistry, Wakayama Medical University, 811-1 Kimiidera, Wakayama, Wakayama 641-0012, Japan; (S.M.); (Y.I.); (M.I.); (K.N.)
| | - Midori Ikezaki
- Department of Biochemistry, Wakayama Medical University, 811-1 Kimiidera, Wakayama, Wakayama 641-0012, Japan; (S.M.); (Y.I.); (M.I.); (K.N.)
| | - Kazuchika Nishitsuji
- Department of Biochemistry, Wakayama Medical University, 811-1 Kimiidera, Wakayama, Wakayama 641-0012, Japan; (S.M.); (Y.I.); (M.I.); (K.N.)
| | - Yukishige Ito
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan;
- RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Yoshito Ihara
- Department of Biochemistry, Wakayama Medical University, 811-1 Kimiidera, Wakayama, Wakayama 641-0012, Japan; (S.M.); (Y.I.); (M.I.); (K.N.)
- Correspondence: ; Tel.: +81-73-441-0628
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7
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Li X, Li S, Huang X, Chen Y, Cheng J, Zhan A. Protein-mediated bioadhesion in marine organisms: A review. MARINE ENVIRONMENTAL RESEARCH 2021; 170:105409. [PMID: 34271483 DOI: 10.1016/j.marenvres.2021.105409] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 07/01/2021] [Accepted: 07/03/2021] [Indexed: 06/13/2023]
Abstract
Protein-mediated bioadhesion is one of the crucial physiological processes in marine organisms, by which they can firmly adhere to underwater substrates. Most marine adhesive organisms are biofoulers, causing negative effects on marine ecosystems and huge economic losses to aquaculture and maritime industries. Furthermore, adhesive proteins in these organisms are promising bionic candidates for high-performance artificial materials with great application value. In-depth understanding of the bioadhesion in marine ecosystems is of dual significance for resolving biofouling issue and developing marine bionic products. Here, we review the research progress of protein-mediated bioadhesion in marine organisms. The adhesion processes such as protein biosynthesis and secretion are similar among organisms, but the detailed features such as compositions, structures, and molecular functions of adhesive proteins are distinct. Hydroxylation, glycosylation, and phosphorylation are important post-translational modifications during the processes of adhesion. The contents of some amino acids such as glycine, tyrosine and cysteine involved in underwater adhesion are significantly higher, which is a sequence feature of barnacle cement and mussel foot proteins. The amyloid structures and conserved domains/motifs such as EGF and vWFA distributed in adhesive proteins are involved in the underwater adhesion. In addition, the oxidative cross-linking also plays an important role in marine bioadhesion. Overall, the unique and common features identified for the protein-mediated bioadhesion in diverse marine organisms here provide background information and essential reference for characterizing marine adhesive proteins and associated functional domains, formulating antifouling strategies, and developing novel biomimetic adhesives.
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Affiliation(s)
- Xi Li
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing, 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing, 100049, China
| | - Shiguo Li
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing, 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing, 100049, China.
| | - Xuena Huang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing, 100085, China
| | - Yiyong Chen
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing, 100085, China
| | - Jiawei Cheng
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing, 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing, 100049, China
| | - Aibin Zhan
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing, 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing, 100049, China.
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8
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Inoue K, Yoshioka Y, Tanaka H, Kinjo A, Sassa M, Ueda I, Shinzato C, Toyoda A, Itoh T. Genomics and Transcriptomics of the green mussel explain the durability of its byssus. Sci Rep 2021; 11:5992. [PMID: 33727571 PMCID: PMC7971044 DOI: 10.1038/s41598-021-84948-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 02/18/2021] [Indexed: 11/09/2022] Open
Abstract
Mussels, which occupy important positions in marine ecosystems, attach tightly to underwater substrates using a proteinaceous holdfast known as the byssus, which is tough, durable, and resistant to enzymatic degradation. Although various byssal proteins have been identified, the mechanisms by which it achieves such durability are unknown. Here we report comprehensive identification of genes involved in byssus formation through whole-genome and foot-specific transcriptomic analyses of the green mussel, Perna viridis. Interestingly, proteins encoded by highly expressed genes include proteinase inhibitors and defense proteins, including lysozyme and lectins, in addition to structural proteins and protein modification enzymes that probably catalyze polymerization and insolubilization. This assemblage of structural and protective molecules constitutes a multi-pronged strategy to render the byssus highly resistant to environmental insults.
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Affiliation(s)
- Koji Inoue
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, 277-8564, Japan.
| | - Yuki Yoshioka
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, 277-8564, Japan.,Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-8563, Japan
| | - Hiroyuki Tanaka
- Department of Biological Information, Tokyo Institute of Technology, Meguro, Tokyo, 152-8550, Japan
| | - Azusa Kinjo
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, 277-8564, Japan
| | - Mieko Sassa
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, 277-8564, Japan.,Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-8563, Japan
| | - Ikuo Ueda
- School of Marine Biosciences, Kitasato University, Kanagawa, 252-0373, Japan.,Faculty of Science, Kanagawa University, Hiratsuka, 259-1293, Japan
| | - Chuya Shinzato
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, 277-8564, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, 411-8540, Japan
| | - Takehiko Itoh
- Department of Biological Information, Tokyo Institute of Technology, Meguro, Tokyo, 152-8550, Japan
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Park S, Kim S, Jho Y, Hwang DS. Cation-π Interactions and Their Contribution to Mussel Underwater Adhesion Studied Using a Surface Forces Apparatus: A Mini-Review. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:16002-16012. [PMID: 31423790 DOI: 10.1021/acs.langmuir.9b01976] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Mussel underwater adhesion is a model phenomenon important for the understanding of broader biological adhesion and the development of biomimetic wet adhesives. The catechol moiety of 3,4-dihydroxyphenyl-l-alanine (DOPA) is known to be actively involved in the mechanism of mussel underwater adhesion; however, other underwater adhesion mechanisms are also crucial. The surface forces apparatus (SFA) has often been used to explore the contributions of other mechanisms to mussel underwater adhesion; e.g., recent SFA-based nanomechanical studies have revealed that cation-π interactions, one of the strongest intermolecular interactions in water, are the pivotal interactions of adhesive proteins involved in underwater mussel adhesion. This mini-review surveys recent research on cation-π interactions and their contributions to strong mussel underwater adhesion, shedding light on some biological processes and facilitating the development of biomedical adhesives.
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Affiliation(s)
- Sohee Park
- Division of Environmental Science and Engineering , Pohang University of Science and Technology (POSTECH) , 77 Chengam-ro, Nam-gu , Pohang 37673 , Republic of Korea
| | - Sangsik Kim
- Division of Environmental Science and Engineering , Pohang University of Science and Technology (POSTECH) , 77 Chengam-ro, Nam-gu , Pohang 37673 , Republic of Korea
- Division of Integrative Biosciences and Biotechnology , Pohang University of Science and Technology (POSTECH) , 77 Chengam-ro, Nam-gu , Pohang 37673 , Republic of Korea
| | - YongSeok Jho
- Department of Physics and Research Institute of Natural Science , Gyeongsang National University , Jinju 52828 , Republic of Korea
| | - Dong Soo Hwang
- Division of Environmental Science and Engineering , Pohang University of Science and Technology (POSTECH) , 77 Chengam-ro, Nam-gu , Pohang 37673 , Republic of Korea
- Division of Integrative Biosciences and Biotechnology , Pohang University of Science and Technology (POSTECH) , 77 Chengam-ro, Nam-gu , Pohang 37673 , Republic of Korea
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Niwa Y, Simizu S. C-Mannosylation: Previous Studies and Future Research Perspectives. TRENDS GLYCOSCI GLYC 2018. [DOI: 10.4052/tigg.1755.1e] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Yuki Niwa
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University
| | - Siro Simizu
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University
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11
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Enrichment and characterization of a bacterial mixture capable of utilizing C-mannosyl tryptophan as a carbon source. Glycoconj J 2018; 35:165-176. [PMID: 29335800 DOI: 10.1007/s10719-017-9807-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2017] [Revised: 11/18/2017] [Accepted: 11/22/2017] [Indexed: 10/18/2022]
Abstract
C-Mannosylation, a protein-modification found in various eukaryotes, involves the attachment of a single mannose molecule to selected tryptophan residues of proteins. Since C-mannosyl tryptophan (CMW) was detected in human urine, it is generally thought that CMW is not catabolized inside our body and instead is excreted via the urine. This paper reports enrichment of a bacterial consortium from soil that degrades CMW. The bacteria grew in minimal medium supplemented with CMW as the carbon source. Interestingly, even after successive clonal picks of individual colonies, several species were still present in each colony as revealed by 16S rRNA gene sequence analysis, indicating that a single species may not be responsible for this activity. A next generation sequencing (NGS) analysis was therefore carried out in order to determine which bacteria were responsible for the catabolism of CMW. It was found that a species of Sphingomonadaceae family, but not others, increased with simultaneous decrease of CMW in the media, suggesting that this species is most likely the one that is actively involved in the degradation of CMW.
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12
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Bouhlel Z, Genard B, Ibrahim N, Carrington E, Babarro JMF, Lok A, Flores AAV, Pellerin C, Tremblay R, Marcotte I. Interspecies comparison of the mechanical properties and biochemical composition of byssal threads. J Exp Biol 2017; 220:984-994. [DOI: 10.1242/jeb.141440] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 12/19/2016] [Indexed: 12/31/2022]
Abstract
Several bivalve species produce byssus threads to provide attachment to substrates, with mechanical properties highly variable among species. Here, we examined the distal section of byssal threads produced by a range of bivalve species (Mytilus edulis, Mytilus trossulus, Mytilus galloprovincialis, Mytilus californianus, Pinna nobilis, Perna perna, Xenostrobus securis, Brachidontes solisianus and Isognomon bicolor) collected from different nearshore environments. Morphological and mechanical properties were measured, and biochemical analyses were performed. Multivariate redundancy analyses on mechanical properties revealed that byssal threads of M. californianus, M. galloprovincialis and P. nobilis have very distinct mechanical behaviors compared to the remaining species. Extensibility, strength and force were the main variables separating these species groups, which were highest for M. californianus and lowest for P. nobilis. Furthermore, the analysis of the amino acid composition revealed that I. bicolor and P. nobilis threads are significantly different from the other species, suggesting a different underlying structural strategy. Determination of metal contents showed that the individual concentration of inorganic elements varies but that the dominant elements are conserved between species. Altogether, this bivalve species comparison suggests some molecular bases for the biomechanical characteristics of byssal fibers that may reflect phylogenetic limitations.
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Affiliation(s)
- Zeineb Bouhlel
- Institut des Science de la Mer, Université du Québec à Rimouski, 310 allée des Ursulines, Rimouski, Québec, G5L 3A1 Canada
| | - Bertrand Genard
- Département de chimie, Université du Québec à Montréal, C.P. 8888, Succursale Centre-Ville, Montréal, Québec, H3C 3P8 Canada
| | - Neilly Ibrahim
- Département de chimie, Université de Montréal, C.P. 6128, Succursale Centre-Ville, Montréal, Québec, H3C 3J7 Canada
| | - Emily Carrington
- Department of Biology and Friday Harbor Laboratories, University of Washington, 620 University Road, Friday Harbor, Washington 98250, USA
| | - José M. F. Babarro
- Instituto de Investigaciones Marinas CSIC, Eduardo Cabello 6, 36208 Vigo, Spain
| | - Aynur Lok
- Aynur Lok, Ege University, Faculty of Fisheries, Genclik Caddesi No: 1235040 Bornova, Izmir, Turkey
| | - Augusto A. V. Flores
- Centro de biologia marinha, Universidade de São Paulo, Rod, Maniel Hipólito, do Rego, São Sebastião, SP, 11600-000, Brazil
| | - Christian Pellerin
- Département de chimie, Université de Montréal, C.P. 6128, Succursale Centre-Ville, Montréal, Québec, H3C 3J7 Canada
| | - Réjean Tremblay
- Institut des Science de la Mer, Université du Québec à Rimouski, 310 allée des Ursulines, Rimouski, Québec, G5L 3A1 Canada
| | - Isabelle Marcotte
- Département de chimie, Université du Québec à Montréal, C.P. 8888, Succursale Centre-Ville, Montréal, Québec, H3C 3P8 Canada
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Rodrigues M, Ostermann T, Kremeser L, Lindner H, Beisel C, Berezikov E, Hobmayer B, Ladurner P. Profiling of adhesive-related genes in the freshwater cnidarian Hydra magnipapillata by transcriptomics and proteomics. BIOFOULING 2016; 32:1115-1129. [PMID: 27661452 PMCID: PMC5080974 DOI: 10.1080/08927014.2016.1233325] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 09/01/2016] [Indexed: 06/06/2023]
Abstract
The differentiated ectodermal basal disc cells of the freshwater cnidarian Hydra secrete proteinaceous glue to temporarily attach themselves to underwater surfaces. Using transcriptome sequencing and a basal disc-specific RNA-seq combined with in situ hybridisation a highly specific set of candidate adhesive genes was identified. A de novo transcriptome assembly of 55,849 transcripts (>200 bp) was generated using paired-end and single reads from Illumina libraries constructed from different polyp conditions. Differential transcriptomics and spatial gene expression analysis by in situ hybridisation allowed the identification of 40 transcripts exclusively expressed in the ectodermal basal disc cells. Comparisons after mass spectrometry analysis of the adhesive secretion showed a total of 21 transcripts to be basal disc specific and eventually secreted through basal disc cells. This is the first study to survey adhesion-related genes in Hydra. The candidate list presented in this study provides a platform for unravelling the molecular mechanism of underwater adhesion of Hydra.
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Affiliation(s)
- Marcelo Rodrigues
- Institute of Zoology and Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
| | - Thomas Ostermann
- Institute of Zoology and Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
| | - Leopold Kremeser
- Division of Clinical Biochemistry, Biocenter, Innsbruck Medical University, Innsbruck, Austria
| | - Herbert Lindner
- Division of Clinical Biochemistry, Biocenter, Innsbruck Medical University, Innsbruck, Austria
| | | | - Eugene Berezikov
- ERIBA, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Bert Hobmayer
- Institute of Zoology and Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
| | - Peter Ladurner
- Institute of Zoology and Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
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Adhesive organ regeneration in Macrostomum lignano. BMC DEVELOPMENTAL BIOLOGY 2016; 16:20. [PMID: 27255153 PMCID: PMC4890501 DOI: 10.1186/s12861-016-0121-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 05/23/2016] [Indexed: 11/19/2022]
Abstract
Background Flatworms possess pluripotent stem cells that can give rise to all cell types, which allows them to restore lost body parts after injury or amputation. This makes flatworms excellent model systems for studying regeneration. In this study, we present the adhesive organs of a marine flatworm as a simple model system for organ regeneration. Macrostomum lignano has approximately 130 adhesive organs at the ventral side of its tail plate. One adhesive organ consists of three interacting cells: one adhesive gland cell, one releasing gland cell, and one modified epidermal cell, called an anchor cell. However, no specific markers for these cell types were available to study the regeneration of adhesive organs. Results We tested 15 commercially available lectins for their ability to label adhesive organs and found one lectin (peanut agglutinin) to be specific to adhesive gland cells. We visualized the morphology of regenerating adhesive organs using lectin- and antibody staining as well as transmission electron microscopy. Our findings indicate that the two gland cells differentiate earlier than the connected anchor cells. Using EdU/lectin staining of partially amputated adhesive organs, we showed that their regeneration can proceed in two ways. First, adhesive gland cell bodies are able to survive partial amputation and reconnect with newly formed anchor cells. Second, adhesive gland cell bodies are cleared away, and the entire adhesive organ is build anew. Conclusion Our results provide the first insights into adhesive organ regeneration and describe ten new markers for differentiated cells and tissues in M. lignano. The position of adhesive organ cells within the blastema and their chronological differentiation have been shown for the first time. M. lignano can regenerate adhesive organs de novo but also replace individual anchor cells in an injured organ. Our findings contribute to a better understanding of organogenesis in flatworms and enable further molecular investigations of cell-fate decisions during regeneration. Electronic supplementary material The online version of this article (doi:10.1186/s12861-016-0121-1) contains supplementary material, which is available to authorized users.
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Toubarro D, Gouveia A, Ribeiro RM, Simões N, da Costa G, Cordeiro C, Santos R. Cloning, Characterization, and Expression Levels of the Nectin Gene from the Tube Feet of the Sea Urchin Paracentrotus Lividus. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2016; 18:372-383. [PMID: 27194026 DOI: 10.1007/s10126-016-9698-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 02/10/2016] [Indexed: 06/05/2023]
Abstract
Marine bioadhesives perform in ways that manmade products simply cannot match, especially in wet environments. Despite their technological potential, bioadhesive molecular mechanisms are still largely understudied, and sea urchin adhesion is no exception. These animals inhabit wave-swept shores, relying on specialized adhesive organs, tube feet, composed by an adhesive disc and a motile stem. The disc encloses a duo-gland adhesive system, producing adhesive and deadhesive secretions for strong reversible substratum attachment. The disclosure of sea urchin Paracentrotus lividus tube foot disc proteome led to the identification of a secreted adhesion protein, Nectin, never before reported in adult adhesive organs but, that given its adhesive function in eggs/embryos, was pointed out as a putative substratum adhesive protein in adults. To further understand Nectin involvement in sea urchin adhesion, Nectin cDNA was amplified for the first time from P. lividus adhesive organs, showing that not only the known Nectin mRNA, called Nectin-1 (GenBank AJ578435), is expressed in the adults tube feet but also a new mRNA sequence, called Nectin-2 (GenBank KT351732), differing in 15 missense nucleotide substitutions. Nectin genomic DNA was also obtained for the first time, indicating that both Nectin-1 and Nectin-2 derive from a single gene. In addition, expression analysis showed that both Nectins are overexpressed in tube feet discs, its expression being significantly higher in tube feet discs from sea urchins just after collection from the field relative to sea urchin from aquarium. These data further advocate for Nectin involvement in sea urchin reversible adhesion, suggesting that its expression might be regulated according to the hydrodynamic conditions.
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Affiliation(s)
- Duarte Toubarro
- Centro de Biotecnologia dos Açores, Departamento de Biologia, Universidade dos Açores, 9501-801, Ponta Delgada, Açores, Portugal
- Structural and Cellular Microbiology Unit, Instituto de Tecnologia Química e Biológica, 2780-157, Oeiras, Portugal
| | - Analuce Gouveia
- Centro de Biotecnologia dos Açores, Departamento de Biologia, Universidade dos Açores, 9501-801, Ponta Delgada, Açores, Portugal
| | - Raquel Mesquita Ribeiro
- Centro de Química e Bioquímica, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal
- Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisboa, Portugal
| | - Nélson Simões
- Centro de Biotecnologia dos Açores, Departamento de Biologia, Universidade dos Açores, 9501-801, Ponta Delgada, Açores, Portugal
| | - Gonçalo da Costa
- Centro de Química e Bioquímica, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal
- Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisboa, Portugal
- Laboratório de FTICR e Espectrometria de Massa Estrutural, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisboa, Portugal
| | - Carlos Cordeiro
- Centro de Química e Bioquímica, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal
- Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisboa, Portugal
- Laboratório de FTICR e Espectrometria de Massa Estrutural, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisboa, Portugal
| | - Romana Santos
- Centro de Química e Bioquímica, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal.
- MARE-Centro de Ciências do Mar e do Ambiente, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal.
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Lebesgue N, da Costa G, Ribeiro RM, Ribeiro-Silva C, Martins GG, Matranga V, Scholten A, Cordeiro C, Heck AJR, Santos R. Deciphering the molecular mechanisms underlying sea urchin reversible adhesion: A quantitative proteomics approach. J Proteomics 2016; 138:61-71. [PMID: 26926440 DOI: 10.1016/j.jprot.2016.02.026] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Revised: 02/22/2016] [Accepted: 02/23/2016] [Indexed: 01/24/2023]
Abstract
UNLABELLED Marine bioadhesives have unmatched performances in wet environments, being an inspiration for biomedical applications. In sea urchins specialized adhesive organs, tube feet, mediate reversible adhesion, being composed by a disc, producing adhesive and de-adhesive secretions, and a motile stem. After tube foot detachment, the secreted adhesive remains bound to the substratum as a footprint. Sea urchin adhesive is composed by proteins and sugars, but so far only one protein, Nectin, was shown to be over-expressed as a transcript in tube feet discs, suggesting its involvement in sea urchin adhesion. Here we use high-resolution quantitative mass-spectrometry to perform the first study combining the analysis of the differential proteome of an adhesive organ, with the proteome of its secreted adhesive. This strategy allowed us to identify 163 highly over-expressed disc proteins, specifically involved in sea urchin reversible adhesion; to find that 70% of the secreted adhesive components fall within five protein groups, involved in exocytosis and microbial protection; and to provide evidences that Nectin is not only highly expressed in tube feet discs but is an actual component of the adhesive. These results give an unprecedented insight into the molecular mechanisms underlying sea urchin adhesion, and opening new doors to develop wet-reliable, reversible, and ecological biomimetic adhesives. SIGNIFICANCE Sea urchins attach strongly but in a reversible manner to substratum, being a valuable source of inspiration for industrial and biomedical applications. Yet, the molecular mechanisms governing reversible adhesion are still poorly studied delaying the engineering of biomimetic adhesives. We used the latest mass spectrometry techniques to analyze the differential proteome of an adhesive organ and the proteome of its secreted adhesive, allowing us to uncover the key players in sea urchin reversible adhesion. We demonstrate, that Nectin, a protein previously pointed out as potentially involved in sea urchin adhesion, is not only highly expressed in tube feet discs, but is a genuine component of the secreted adhesive.
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Affiliation(s)
- Nicolas Lebesgue
- Netherlands Proteomics Center, Padualaan 8, 3584, CH, Utrecht, Netherlands; Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584, CH, Utrecht, Netherlands
| | - Gonçalo da Costa
- Centro de Química e Bioquímica, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, Campo Grande, 1749-016, Lisboa, Portugal; Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisboa, Portugal; Laboratório de FTICR e espectrometria de massa estrutural, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisboa, Portugal
| | - Raquel Mesquita Ribeiro
- Centro de Química e Bioquímica, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, Campo Grande, 1749-016, Lisboa, Portugal; Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisboa, Portugal
| | - Cristina Ribeiro-Silva
- Centro de Química e Bioquímica, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, Campo Grande, 1749-016, Lisboa, Portugal; Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisboa, Portugal
| | - Gabriel G Martins
- Instituto Gulbenkian de Ciência, R. da Quinta Grande 6, 2780-156 Oeiras, Portugal; Centro de Ecologia, Evolução e Alterações Ambientais, Faculdade de Ciências da Universidade de Lisboa, Campo Grande 1749-016, Lisboa, Portugal
| | - Valeria Matranga
- Consiglio Nazionale delle Ricerche, Istituto di Biomedicina e Immunologia Molecolare, 'Alberto Monroy', Via Ugo La Malfa 153, 90146 Palermo, Italy
| | - Arjen Scholten
- Netherlands Proteomics Center, Padualaan 8, 3584, CH, Utrecht, Netherlands; Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584, CH, Utrecht, Netherlands
| | - Carlos Cordeiro
- Centro de Química e Bioquímica, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, Campo Grande, 1749-016, Lisboa, Portugal; Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisboa, Portugal; Laboratório de FTICR e espectrometria de massa estrutural, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisboa, Portugal
| | - Albert J R Heck
- Netherlands Proteomics Center, Padualaan 8, 3584, CH, Utrecht, Netherlands; Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584, CH, Utrecht, Netherlands
| | - Romana Santos
- Centro de Química e Bioquímica, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, Campo Grande, 1749-016, Lisboa, Portugal; MARE - Centro de Ciências do Mar e do Ambiente, Faculdade de Ciências da Universidade de Lisboa, Campo Grande 1749-016, Lisboa, Portugal.
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Yoo HY, Song YH, Seo JH, Cha HJ, Hwang DS. Recombinant mussel coating protein fused with cell adhesion recognition motif enhanced cell proliferation. BIOTECHNOL BIOPROC E 2015. [DOI: 10.1007/s12257-014-0621-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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18
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Hennebert E, Maldonado B, Ladurner P, Flammang P, Santos R. Experimental strategies for the identification and characterization of adhesive proteins in animals: a review. Interface Focus 2015; 5:20140064. [PMID: 25657842 PMCID: PMC4275877 DOI: 10.1098/rsfs.2014.0064] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Adhesive secretions occur in both aquatic and terrestrial animals, in which they perform diverse functions. Biological adhesives can therefore be remarkably complex and involve a large range of components with different functions and interactions. However, being mainly protein based, biological adhesives can be characterized by classical molecular methods. This review compiles experimental strategies that were successfully used to identify, characterize and obtain the full-length sequence of adhesive proteins from nine biological models: echinoderms, barnacles, tubeworms, mussels, sticklebacks, slugs, velvet worms, spiders and ticks. A brief description and practical examples are given for a variety of tools used to study adhesive molecules at different levels from genes to secreted proteins. In most studies, proteins, extracted from secreted materials or from adhesive organs, are analysed for the presence of post-translational modifications and submitted to peptide sequencing. The peptide sequences are then used directly for a BLAST search in genomic or transcriptomic databases, or to design degenerate primers to perform RT-PCR, both allowing the recovery of the sequence of the cDNA coding for the investigated protein. These sequences can then be used for functional validation and recombinant production. In recent years, the dual proteomic and transcriptomic approach has emerged as the best way leading to the identification of novel adhesive proteins and retrieval of their complete sequences.
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Affiliation(s)
- Elise Hennebert
- Biology of Marine Organisms and Biomimetics, Research Institute for Biosciences , University of Mons , 23 Place du Parc, 7000 Mons , Belgium
| | - Barbara Maldonado
- Molecular Biology and Genetic Engineering, GIGA-R , University of Liège , 1 Avenue de l'Hôpital, 4000 Liège , Belgium
| | - Peter Ladurner
- Institute of Zoology and Center of Molecular Bioscience Innsbruck , University of Innsbruck , Technikerstrasse 25, 6020 Innsbruck , Austria
| | - Patrick Flammang
- Biology of Marine Organisms and Biomimetics, Research Institute for Biosciences , University of Mons , 23 Place du Parc, 7000 Mons , Belgium
| | - Romana Santos
- Unidade de Investigação em Ciências Orais e Biomédicas, Faculdade de Medicina Dentária , Universidade de Lisboa, Cidade Universitária , 1649-003 Lisboa , Portugal
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Leung PTY, Ip JCH, Mak SST, Qiu JW, Lam PKS, Wong CKC, Chan LL, Leung KMY. De novo transcriptome analysis of Perna viridis highlights tissue-specific patterns for environmental studies. BMC Genomics 2014; 15:804. [PMID: 25239240 PMCID: PMC4190305 DOI: 10.1186/1471-2164-15-804] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 08/26/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The tropical green-lipped mussel Perna viridis is a common biomonitor throughout the Indo-Pacific region that is used for environmental monitoring and ecotoxicological investigations. However, there is limited molecular data available regarding this species. We sought to establish a global transcriptome database from the tissues of adductor muscle, gills and the hepatopancreas of P. viridis in an effort to advance our understanding of the molecular aspects involved during specific toxicity responses in this sentinel species. RESULTS Illumina sequencing results yielded 544,272,542 high-quality filtered reads. After de novo assembly using Trinity, 233,257 contigs were generated with an average length of 1,264 bp and an N50 length of 2,868 bp; 192,879 assembled transcripts and 150,111 assembled unigenes were obtained after clustering. A total of 93,668 assembled transcripts (66,692 assembled genes) with putative functions for protein domains were predicted based on InterProScan analysis. Based on similarity searches, 44,713 assembled transcripts and 25,319 assembled unigenes were annotated with at least one BLAST hit. A total of 21,262 assembled transcripts (11,947 assembled genes) were annotated with at least one well-defined Gene Ontology (GO) and 5,131 assembled transcripts (3,181 assembled unigenes) were assigned to 329 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. The quantity of assembled unigenes and transcripts obtained from male and female mussels were similar but varied among the three studied tissues, with the highest numbers recorded in the gills, followed by the hepatopancreas, and then the adductor muscle. Multivariate analyses revealed strong tissue-specific patterns among the three different tissues, but not between sexes in terms of expression profiles for annotated genes in various GO terms, and genes associated with stress responses and degradation of xenobiotics. The expression profiles of certain selected genes in each tissue type were further validated using real-time quantitative polymerase chain reaction assays and a similar tissue-specific trend was seen. CONCLUSIONS The extensive sequence data generated from this study will provide a valuable molecular resource for facilitating environmental studies with P. viridis, and highlight the importance of tissue-specific approaches in the future.
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Affiliation(s)
| | | | | | | | | | | | | | - Kenneth M Y Leung
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China.
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20
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Hagenau A, Suhre MH, Scheibel TR. Nature as a blueprint for polymer material concepts: Protein fiber-reinforced composites as holdfasts of mussels. Prog Polym Sci 2014. [DOI: 10.1016/j.progpolymsci.2014.02.007] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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21
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Kasson TMD, Barry BA. Reactive oxygen and oxidative stress: N-formyl kynurenine in photosystem II and non-photosynthetic proteins. PHOTOSYNTHESIS RESEARCH 2012; 114:97-110. [PMID: 23161228 DOI: 10.1007/s11120-012-9784-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2012] [Accepted: 10/31/2012] [Indexed: 06/01/2023]
Abstract
While light is the essential driving force for photosynthetic carbon fixation, high light intensities are toxic to photosynthetic organisms. Prolonged exposure to high light results in damage to the photosynthetic membrane proteins and suboptimal activity, a phenomenon called photoinhibition. The primary target for inactivation is the photosystem II (PSII) reaction center. PSII catalyzes the light-induced oxidation of water at the oxygen-evolving complex. Reactive oxygen species (ROS) are generated under photoinhibitory conditions and induce oxidative post translational modifications of amino acid side chains. Specific modification of tryptophan residues to N-formylkynurenine (NFK) occurs in the CP43 and D1 core polypeptides of PSII. The NFK modification has also been detected in other proteins, such as mitochondrial respiratory enzymes, and is formed by a non-random, ROS-targeted mechanism. NFK has been shown to accumulate in PSII during conditions of high light stress in vitro. This review provides a summary of what is known about the generation and function of NFK in PSII and other proteins. Currently, the role of ROS in photoinhibition is under debate. Furthermore, the triggers for the degradation and accelerated turnover of PSII subunits, which occur under high light, are not yet identified. Owing to its unique optical and Raman signal, NFK provides a new marker to use in the identification of ROS generation sites in PSII and other proteins. Also, the speculative hypothesis that NFK, and other oxidative modifications of tryptophan, play a role in the PSII damage and repair cycle is discussed. NFK may have a similar function during oxidative stress in other biologic systems.
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Affiliation(s)
- Tina M Dreaden Kasson
- School of Chemistry and Biochemistry and Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
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22
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A novel recombinant bioadhesive designed from the non-repeating region of Perna viridis foot protein-1. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2012. [DOI: 10.1016/j.msec.2012.04.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Abstract
Glycosylation represents the most complex co- and post-translational modification of proteins. In addition to N- and O-glycans, almost all combinations, including the nature of the carbohydrate moiety and the amino-acid involved, but also the type of the chemical linkage, can be isolated from natural glycoconjugates. This diversity correlates with the importance and the variety of the biological processes (and consequently the diseases) glycosides are involved in. This review focuses on rare and unusual glycosylation of peptides and proteins.
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Affiliation(s)
- Pierre Lafite
- Institut de Chimie Organique et Analytique-ICOA, Université d'Orléans, UMR CNRS 7311, Rue de Chartres, BP 6759, 45067 Orléans Cedex 2, France
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Hwang DS, Zeng H, Lu Q, Israelachvili J, Waite JH. Adhesion mechanism in a DOPA-deficient foot protein from green mussels(). SOFT MATTER 2012; 8:5640-5648. [PMID: 23105946 PMCID: PMC3482130 DOI: 10.1039/c2sm25173f] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
The holdfast or byssus of Asian green mussels, Perna viridis, contains a foot protein, pvfp-1, that differs in two respects from all other known adhesive mussel foot proteins (mfp): (1) instead of the hallmark L-3,4-dihydroxyphenylalanine (DOPA) residues in mfp-1, for example, pvfp-1 contains C(2)-mannosyl-7-hydroxytryptophan (Man7OHTrp). (2) In addition, pvfp-1 chains are not monomeric like mfp-1 but trimerized by collagen and coiled-coil domains near the carboxy terminus after a typical domain of tandemly repeated decapeptides. Here, the contribution of these peculiarities to adhesion was examined using a surface forces apparatus (SFA). Unlike previously studied mfp-1s, pvfp-1 showed significant adhesion to mica and, in symmetric pvfp-1 films, substantial cohesive interactions were present at pH 5.5. The role of Man7OHTrp in adhesion is not clear, and a DOPA-like role for Man7OHTrp in metal complexation (e.g., Cu(2+), Fe(3+)) was not observed. Instead, cation-π interactions with low desolvation penalty between Man7OHTrp and lysyl side chains and conformational changes (raveling and unraveling of collagen helix and coiled-coil domains) are the best explanations for the strong adhesion between pvfp-1 monomolecular films. The strong adhesion mechanism induced by cation-π interactions and conformational changes in pvfp-1 provides new insights for the development of biomimetic underwater adhesives.
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Affiliation(s)
- Dong Soo Hwang
- Ocean Science and Technology Institute, Pohang University of Science and Technology, Hyoja-Dong, Nam-Gu, Pohang, Gyeongbuk, 790-784, Korea
- Materials Research Laboratory, University of California, Santa Barbara, CA 93106, USA
| | - Hongbo Zeng
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, AB, T6G 2V4 Canada. Fax: +1-780-492-2881; Tel: +1-780-492-1044
| | - Qingye Lu
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, AB, T6G 2V4 Canada. Fax: +1-780-492-2881; Tel: +1-780-492-1044
| | - Jacob Israelachvili
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, USA
- Materials Research Laboratory, University of California, Santa Barbara, CA 93106, USA
| | - J. Herbert Waite
- Materials Research Laboratory, University of California, Santa Barbara, CA 93106, USA
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Barbara, CA 93106, USA
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Barlow DE, Wahl KJ. Optical spectroscopy of marine bioadhesive interfaces. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2012; 5:229-51. [PMID: 22524229 DOI: 10.1146/annurev-anchem-061010-113844] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Marine organisms have evolved extraordinarily effective adhesives that cure underwater and resist degradation. These underwater adhesives differ dramatically in structure and function and are composed of multiple proteins assembled into functional composites. The processes by which these bioadhesives cure--conformational changes, dehydration, polymerization, and cross-linking--are challenging to quantify because they occur not only underwater but also in a buried interface between the substrate and the organism. In this review, we highlight interfacial optical spectroscopy approaches that can reveal the biochemical processes and structure of marine bioadhesives, with particular emphasis on macrofoulers such as barnacles and mussels.
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Affiliation(s)
- Daniel E Barlow
- Chemistry Division, U.S. Naval Research Laboratory, Washington, DC 20375-5342, USA
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Kamino K, Nakano M, Kanai S. Significance of the conformation of building blocks in curing of barnacle underwater adhesive. FEBS J 2012; 279:1750-60. [DOI: 10.1111/j.1742-4658.2012.08552.x] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Molecular interactions of mussel protective coating protein, mcfp-1, from Mytilus californianus. Biomaterials 2012; 33:1903-11. [DOI: 10.1016/j.biomaterials.2011.11.021] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2011] [Accepted: 11/13/2011] [Indexed: 11/16/2022]
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Dreaden TM, Chen J, Rexroth S, Barry BA. N-formylkynurenine as a marker of high light stress in photosynthesis. J Biol Chem 2011; 286:22632-41. [PMID: 21527632 PMCID: PMC3121407 DOI: 10.1074/jbc.m110.212928] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2010] [Revised: 04/28/2011] [Indexed: 11/06/2022] Open
Abstract
Photosystem II (PSII) is the membrane protein complex that catalyzes the photo-induced oxidation of water at a manganese-calcium active site. Light-dependent damage and repair occur in PSII under conditions of high light stress. The core reaction center complex is composed of the D1, D2, CP43, and CP47 intrinsic polypeptides. In this study, a new chromophore formed from the oxidative post-translational modification of tryptophan is identified in the CP43 subunit. Tandem mass spectrometry peptide sequencing is consistent with the oxidation of the CP43 tryptophan side chain, Trp-365, to produce N-formylkynurenine (NFK). Characterization with ultraviolet visible absorption and ultraviolet resonance Raman spectroscopy supports this assignment. An optical assay suggests that the yield of NFK increases 2-fold (2.2 ± 0.5) under high light illumination. A concomitant 2.4 ± 0.5-fold decrease is observed in the steady-state rate of oxygen evolution under the high light conditions. NFK is the product formed from reaction of tryptophan with singlet oxygen, which can be produced under high light stress in PSII. Reactive oxygen species reactions lead to oxidative damage of the reaction center, D1 protein turnover, and inhibition of electron transfer. Our results are consistent with a role for the CP43 NFK modification in photoinhibition.
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Affiliation(s)
- Tina M. Dreaden
- From the School of Chemistry and Biochemistry and the Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332
| | - Jun Chen
- From the School of Chemistry and Biochemistry and the Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332
| | - Sascha Rexroth
- From the School of Chemistry and Biochemistry and the Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332
| | - Bridgette A. Barry
- From the School of Chemistry and Biochemistry and the Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332
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Hennebert E, Wattiez R, Flammang P. Characterisation of the carbohydrate fraction of the temporary adhesive secreted by the tube feet of the sea star Asterias rubens. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2011; 13:484-495. [PMID: 20886254 DOI: 10.1007/s10126-010-9319-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2010] [Accepted: 09/08/2010] [Indexed: 05/29/2023]
Abstract
In sea stars, adhesion takes place at the level of a multitude of small appendages, the tube feet. It involves the secretion of an adhesive material which, after tube foot detachment, remains on the substratum as a footprint. It was previously reported that the two main organic components of this material are proteins and carbohydrates. The carbohydrate moiety of the adhesive secretion of Asterias rubens was investigated using a set of 16 lectins which were used on sections through tube feet, on footprints, and on the proteins extracted from these footprints. After gel electrophoresis, these proteins separate into eight protein bands which were named sea star footprint proteins (Sfps). Eleven lectins label the tube foot epidermis at the level of the adhesive cells, four react with footprints, and eight with two of the extracted footprint proteins, which are therefore classified as glycoproteins. Sfp-290 appears to bear mostly N-linked oligosaccharides and Sfp-210 principally O-linked oligosaccharides. The outer chains of both glycoproteins enclose galactose, N-acetylgalactosamine, fucose, and sialic acid residues. Another part of the carbohydrate fraction of the footprints would be in the form of larger molecules, such as sialylated proteoglycans. These two types of glycoconjugates are presumably key components of the sea star temporary adhesive providing both cohesive and adhesive contributions through electrostatic interactions by the polar and hydrogen-bonding functional groups of their glycan chains.
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Affiliation(s)
- Elise Hennebert
- Laboratoire de Biologie Marine, Université de Mons-UMONS, Pentagone 2B 6, Avenue du Champ de Mars, 7000, Mons, Belgium
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Ihara Y, Inai Y, Ikezaki M. Protein C-Mannosylation and Its Prospective Functions in the Cell. TRENDS GLYCOSCI GLYC 2011. [DOI: 10.4052/tigg.23.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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