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Guevara T, Körschgen H, Cuppari A, Schmitz C, Kuske M, Yiallouros I, Floehr J, Jahnen-Dechent W, Stöcker W, Gomis-Rüth FX. The C-terminal region of human plasma fetuin-B is dispensable for the raised-elephant-trunk mechanism of inhibition of astacin metallopeptidases. Sci Rep 2019; 9:14683. [PMID: 31604990 PMCID: PMC6789097 DOI: 10.1038/s41598-019-51095-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 09/24/2019] [Indexed: 01/07/2023] Open
Abstract
Human fetuin-B plays a key physiological role in human fertility through its inhibitory action on ovastacin, a member of the astacin family of metallopeptidases. The inhibitor consists of tandem cystatin-like domains (CY1 and CY2), which are connected by a linker containing a "CPDCP-trunk" and followed by a C-terminal region (CTR) void of regular secondary structure. Here, we solved the crystal structure of the complex of the inhibitor with archetypal astacin from crayfish, which is a useful model of human ovastacin. Two hairpins from CY2, the linker, and the tip of the "legumain-binding loop" of CY1 inhibit crayfish astacin following the "raised-elephant-trunk mechanism" recently reported for mouse fetuin-B. This inhibition is exerted by blocking active-site cleft sub-sites upstream and downstream of the catalytic zinc ion, but not those flanking the scissile bond. However, contrary to the mouse complex, which was obtained with fetuin-B nicked at a single site but otherwise intact, most of the CTR was proteolytically removed during crystallization of the human complex. Moreover, the two complexes present in the crystallographic asymmetric unit diverged in the relative arrangement of CY1 and CY2, while the two complexes found for the mouse complex crystal structure were equivalent. Biochemical studies in vitro confirmed the differential cleavage susceptibility of human and mouse fetuin-B in front of crayfish astacin and revealed that the cleaved human inhibitor blocks crayfish astacin and human meprin α and β only slightly less potently than the intact variant. Therefore, the CTR of animal fetuin-B orthologs may have a function in maintaining a particular relative orientation of CY1 and CY2 that nonetheless is dispensable for peptidase inhibition.
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Affiliation(s)
- Tibisay Guevara
- Proteolysis Lab, Department of Structural Biology, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, Helix Building, c/ Baldiri Reixac, 15-21, E-08028, Barcelona, Catalonia, Spain
| | - Hagen Körschgen
- Institute of Molecular Physiology, Cell and Matrix Biology, Johannes Gutenberg-University Mainz, Johann-Joachim-Becher-Weg 7, D-55128, Mainz, Germany
| | - Anna Cuppari
- Proteolysis Lab, Department of Structural Biology, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, Helix Building, c/ Baldiri Reixac, 15-21, E-08028, Barcelona, Catalonia, Spain
| | - Carlo Schmitz
- Biointerface Laboratory, Helmholtz Institute for Biomedical Engineering, RWTH Aachen University Medical Faculty, Pauwelsstr. 30, D-52074, Aachen, Germany
| | - Michael Kuske
- Institute of Molecular Physiology, Cell and Matrix Biology, Johannes Gutenberg-University Mainz, Johann-Joachim-Becher-Weg 7, D-55128, Mainz, Germany
| | - Irene Yiallouros
- Institute of Molecular Physiology, Cell and Matrix Biology, Johannes Gutenberg-University Mainz, Johann-Joachim-Becher-Weg 7, D-55128, Mainz, Germany
| | - Julia Floehr
- Biointerface Laboratory, Helmholtz Institute for Biomedical Engineering, RWTH Aachen University Medical Faculty, Pauwelsstr. 30, D-52074, Aachen, Germany
| | - Willi Jahnen-Dechent
- Biointerface Laboratory, Helmholtz Institute for Biomedical Engineering, RWTH Aachen University Medical Faculty, Pauwelsstr. 30, D-52074, Aachen, Germany
| | - Walter Stöcker
- Institute of Molecular Physiology, Cell and Matrix Biology, Johannes Gutenberg-University Mainz, Johann-Joachim-Becher-Weg 7, D-55128, Mainz, Germany
| | - F Xavier Gomis-Rüth
- Proteolysis Lab, Department of Structural Biology, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, Helix Building, c/ Baldiri Reixac, 15-21, E-08028, Barcelona, Catalonia, Spain.
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Dholey Y, Chaudhuri A, Sen Chakraborty S. An integrated in silico approach to understand protein-protein interactions: human meprin-β with fetuin-A. J Biomol Struct Dyn 2019; 38:2080-2092. [PMID: 31184526 DOI: 10.1080/07391102.2019.1626284] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Human meprin-β, a zinc metalloprotease belonging to the astacin family, have been found to be associated with many pathological conditions like inflammatory bowel disease, fibrosis and neurodegenerative disease. The inhibition of meprin-β by various inhibitors, both macromolecular and small molecules, is crucial in the control of several diseases. Human fetuin-A, a negative acute phase protein involved in inflammatory disease, has recently been identified as an endogenous inhibitor for meprin-β. In this computational study, an integrated in silico approach was performed using existing structural information of meprin-β coupled with ab initio modelling of human fetuin-A to predict a rational model of the complex through protein-protein docking. Further, the models were optimized and validated to generate an ensemble of conformations through extensive molecular dynamics simulation. Virtual alanine scanning mutagenesis was explored to identify hotspot residues on both proteins significant for protein-protein interaction (PPI). The results of the study provide structural insight into PPI between meprin-β and fetuin-A which can be useful in designing molecules to modulate meprin-β activity. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Yuthika Dholey
- Department of Microbiology, West Bengal State University, Kolkata, West Bengal, India
| | - Ankur Chaudhuri
- Department of Microbiology, West Bengal State University, Kolkata, West Bengal, India
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Cuppari A, Körschgen H, Fahrenkamp D, Schmitz C, Guevara T, Karmilin K, Kuske M, Olf M, Dietzel E, Yiallouros I, de Sanctis D, Goulas T, Weiskirchen R, Jahnen-Dechent W, Floehr J, Stoecker W, Jovine L, Gomis-Rüth FX. Structure of mammalian plasma fetuin-B and its mechanism of selective metallopeptidase inhibition. IUCRJ 2019; 6:317-330. [PMID: 30867929 PMCID: PMC6400186 DOI: 10.1107/s2052252519001568] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 01/28/2019] [Indexed: 06/09/2023]
Abstract
Mammalian fetuin-A and fetuin-B are abundant serum proteins with pleiotropic functions. Fetuin-B is a highly selective and potent inhibitor of metallo-peptidases (MPs) of the astacin family, which includes ovastacin in mammals. By inhibiting ovastacin, fetuin-B is essential for female fertility. The crystal structure of fetuin-B was determined unbound and in complex with archetypal astacin, and it was found that the inhibitor has tandem cystatin-type modules (CY1 and CY2). They are connected by an exposed linker with a rigid, disulfide-linked 'CPDCP-trunk', and are followed by a C-terminal region (CTR) with little regular secondary structure. The CPDCP-trunk and a hairpin of CY2 form a bipartite wedge, which slots into the active-site cleft of the MP. These elements occupy the nonprimed and primed sides of the cleft, respectively, but spare the specificity pocket so that the inhibitor is not cleaved. The aspartate in the trunk blocks the catalytic zinc of astacin, while the CY2 hairpin binds through a QWVXGP motif. The CY1 module assists in structural integrity and the CTR is not involved in inhibition, as verified by in vitro studies using a cohort of mutants and variants. Overall, the inhibition conforms to a novel 'raised-elephant-trunk' mechanism for MPs, which is reminiscent of single-domain cystatins that target cysteine peptidases. Over 200 sequences from vertebrates have been annotated as fetuin-B, underpinning its ubiquity and physiological relevance; accordingly, sequences with conserved CPDCP- and QWVXGP-derived motifs have been found from mammals to cartilaginous fishes. Thus, the raised-elephant-trunk mechanism is likely to be generally valid for the inhibition of astacins by orthologs of fetuin-B.
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Affiliation(s)
- Anna Cuppari
- Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, Helix Building, c/o Baldiri Reixac 15-21, E-08028 Barcelona, Catalonia, Spain
| | - Hagen Körschgen
- Institute of Molecular Physiology, Cell and Matrix Biology, Johannes Gutenberg-University Mainz, Johann-Joachim-Becher-Weg 7, D-55128 Mainz, Germany
| | - Dirk Fahrenkamp
- Department of Biosciences and Nutrition and Center for Innovative Medicine, Karolinska Institutet, Blickagången 16, SE-141 83 Huddinge, Sweden
| | - Carlo Schmitz
- Biointerface Laboratory, Helmholtz Institute for Biomedical Engineering, RWTH Aachen University Medical Faculty, Pauwelsstrasse 30, D-52074 Aachen, Germany
| | - Tibisay Guevara
- Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, Helix Building, c/o Baldiri Reixac 15-21, E-08028 Barcelona, Catalonia, Spain
| | - Konstantin Karmilin
- Institute of Molecular Physiology, Cell and Matrix Biology, Johannes Gutenberg-University Mainz, Johann-Joachim-Becher-Weg 7, D-55128 Mainz, Germany
| | - Michael Kuske
- Institute of Molecular Physiology, Cell and Matrix Biology, Johannes Gutenberg-University Mainz, Johann-Joachim-Becher-Weg 7, D-55128 Mainz, Germany
| | - Mario Olf
- Institute of Molecular Physiology, Cell and Matrix Biology, Johannes Gutenberg-University Mainz, Johann-Joachim-Becher-Weg 7, D-55128 Mainz, Germany
| | - Eileen Dietzel
- Department of Biosciences and Nutrition and Center for Innovative Medicine, Karolinska Institutet, Blickagången 16, SE-141 83 Huddinge, Sweden
| | - Irene Yiallouros
- Institute of Molecular Physiology, Cell and Matrix Biology, Johannes Gutenberg-University Mainz, Johann-Joachim-Becher-Weg 7, D-55128 Mainz, Germany
| | - Daniele de Sanctis
- ESRF – The European Synchrotron, 71 Rue Jules Horowitz, F-38000 Grenoble, France
| | - Theodoros Goulas
- Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, Helix Building, c/o Baldiri Reixac 15-21, E-08028 Barcelona, Catalonia, Spain
| | - Ralf Weiskirchen
- Institute of Molecular Pathobiochemistry, Experimental Gene Therapy and Clinical Chemistry, RWTH Aachen University Hospital, Pauwelsstrasse 30, D-52074 Aachen, Germany
| | - Willi Jahnen-Dechent
- Biointerface Laboratory, Helmholtz Institute for Biomedical Engineering, RWTH Aachen University Medical Faculty, Pauwelsstrasse 30, D-52074 Aachen, Germany
| | - Julia Floehr
- Biointerface Laboratory, Helmholtz Institute for Biomedical Engineering, RWTH Aachen University Medical Faculty, Pauwelsstrasse 30, D-52074 Aachen, Germany
| | - Walter Stoecker
- Institute of Molecular Physiology, Cell and Matrix Biology, Johannes Gutenberg-University Mainz, Johann-Joachim-Becher-Weg 7, D-55128 Mainz, Germany
| | - Luca Jovine
- Department of Biosciences and Nutrition and Center for Innovative Medicine, Karolinska Institutet, Blickagången 16, SE-141 83 Huddinge, Sweden
| | - F. Xavier Gomis-Rüth
- Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, Helix Building, c/o Baldiri Reixac 15-21, E-08028 Barcelona, Catalonia, Spain
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Karmilin K, Schmitz C, Kuske M, Körschgen H, Olf M, Meyer K, Hildebrand A, Felten M, Fridrich S, Yiallouros I, Becker-Pauly C, Weiskirchen R, Jahnen-Dechent W, Floehr J, Stöcker W. Mammalian plasma fetuin-B is a selective inhibitor of ovastacin and meprin metalloproteinases. Sci Rep 2019; 9:546. [PMID: 30679641 PMCID: PMC6346019 DOI: 10.1038/s41598-018-37024-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 11/28/2018] [Indexed: 11/29/2022] Open
Abstract
Vertebrate fetuins are multi-domain plasma-proteins of the cystatin-superfamily. Human fetuin-A is also known as AHSG, α2-Heremans-Schmid-glycoprotein. Gene-knockout in mice identified fetuin-A as essential for calcified-matrix-metabolism and bone-mineralization. Fetuin-B deficient mice, on the other hand, are female infertile due to zona pellucida ‘hardening’ caused by the metalloproteinase ovastacin in unfertilized oocytes. In wildtype mice fetuin-B inhibits the activity of ovastacin thus maintaining oocytes fertilizable. Here we asked, if fetuins affect further proteases as might be expected from their evolutionary relation to single-domain-cystatins, known as proteinase-inhibitors. We show that fetuin-A is not an inhibitor of any tested protease. In stark contrast, the closely related fetuin-B selectively inhibits astacin-metalloproteinases such as meprins and ovastacin, but not astacins of the tolloid-subfamily, nor any other proteinase. The analysis of fetuin-B expressed in various mammalian cell types, insect cells, and truncated fish-fetuin expressed in bacteria, showed that the cystatin-like domains alone are necessary and sufficient for inhibition. This report highlights fetuin-B as a specific antagonist of ovastacin and meprin-metalloproteinases. Control of ovastacin was shown to be indispensable for female fertility. Meprin inhibition, on the other hand, renders fetuin-B a potential key-player in proteolytic networks controlling angiogenesis, immune-defense, extracellular-matrix-assembly and general cell-signaling, with implications for inflammation, fibrosis, neurodegenerative disorders and cancer.
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Affiliation(s)
- Konstantin Karmilin
- Institute of Molecular Physiology, Cell and Matrix Biology, Johannes Gutenberg University Mainz, 55099, Mainz, Germany
| | - Carlo Schmitz
- Helmholtz Institute for Biomedical Engineering, Biointerface Laboratory, RWTH Aachen University, Medical Faculty, 52074, Aachen, Germany
| | - Michael Kuske
- Institute of Molecular Physiology, Cell and Matrix Biology, Johannes Gutenberg University Mainz, 55099, Mainz, Germany
| | - Hagen Körschgen
- Institute of Molecular Physiology, Cell and Matrix Biology, Johannes Gutenberg University Mainz, 55099, Mainz, Germany
| | - Mario Olf
- Institute of Molecular Physiology, Cell and Matrix Biology, Johannes Gutenberg University Mainz, 55099, Mainz, Germany
| | - Katharina Meyer
- Institute of Molecular Physiology, Cell and Matrix Biology, Johannes Gutenberg University Mainz, 55099, Mainz, Germany
| | - André Hildebrand
- Institute of Molecular Physiology, Cell and Matrix Biology, Johannes Gutenberg University Mainz, 55099, Mainz, Germany
| | - Matthias Felten
- Institute of Molecular Physiology, Cell and Matrix Biology, Johannes Gutenberg University Mainz, 55099, Mainz, Germany
| | - Sven Fridrich
- Institute of Molecular Physiology, Cell and Matrix Biology, Johannes Gutenberg University Mainz, 55099, Mainz, Germany
| | - Irene Yiallouros
- Institute of Molecular Physiology, Cell and Matrix Biology, Johannes Gutenberg University Mainz, 55099, Mainz, Germany
| | | | - Ralf Weiskirchen
- Institute of Molecular Pathobiochemistry, Experimental Gene Therapy and Clinical Chemistry RWTH, 52074, Aachen, Germany
| | - Willi Jahnen-Dechent
- Helmholtz Institute for Biomedical Engineering, Biointerface Laboratory, RWTH Aachen University, Medical Faculty, 52074, Aachen, Germany
| | - Julia Floehr
- Helmholtz Institute for Biomedical Engineering, Biointerface Laboratory, RWTH Aachen University, Medical Faculty, 52074, Aachen, Germany
| | - Walter Stöcker
- Institute of Molecular Physiology, Cell and Matrix Biology, Johannes Gutenberg University Mainz, 55099, Mainz, Germany.
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Di Q, Lin Q, Huang Z, Chi Y, Chen X, Zhang W, Zhang Y. Zebrafish nephrosin helps host defence against Escherichia coli infection. Open Biol 2018; 7:rsob.170040. [PMID: 28835569 PMCID: PMC5577445 DOI: 10.1098/rsob.170040] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 07/25/2017] [Indexed: 12/20/2022] Open
Abstract
Neutrophils play important roles in innate immunity and are mainly dependent on various enzyme-containing granules to kill engulfed microorganisms. Zebrafish nephrosin (npsn) is specifically expressed in neutrophils; however, its function is largely unknown. Here, we generated an npsn mutant (npsnsmu5) via CRISPR/Cas9 to investigate the in vivo function of Npsn. The overall development and number of neutrophils remained unchanged in npsn-deficient mutants, whereas neutrophil antibacterial function was defective. Upon infection with Escherichia coli, the npsnsmu5 mutants exhibited a lower survival rate and more severe bacterial burden, as well as augmented inflammatory response to challenge with infection when compared with wild-type embryos, whereas npsn-overexpressing zebrafish exhibited enhanced host defence against E. coli infection. These findings demonstrated that zebrafish Npsn promotes host defence against bacterial infection. Furthermore, our findings suggested that npsn-deficient and -overexpressing zebrafish might serve as effective models of in vivo innate immunity.
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Affiliation(s)
- Qianqian Di
- Key Laboratory of Zebrafish Modeling and Drug Screening for Human Diseases of Guangdong Higher Education Institutes, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, People's Republic of China
| | - Qing Lin
- Key Laboratory of Zebrafish Modeling and Drug Screening for Human Diseases of Guangdong Higher Education Institutes, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, People's Republic of China.,Laboratory of Developmental Biology and Regenerative Medicine, School of Medicine, South China University of Technology, Guangzhou 510006, People's Republic of China
| | - Zhibin Huang
- Key Laboratory of Zebrafish Modeling and Drug Screening for Human Diseases of Guangdong Higher Education Institutes, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, People's Republic of China
| | - Yali Chi
- Key Laboratory of Zebrafish Modeling and Drug Screening for Human Diseases of Guangdong Higher Education Institutes, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, People's Republic of China
| | - Xiaohui Chen
- Key Laboratory of Zebrafish Modeling and Drug Screening for Human Diseases of Guangdong Higher Education Institutes, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, People's Republic of China
| | - Wenqing Zhang
- Key Laboratory of Zebrafish Modeling and Drug Screening for Human Diseases of Guangdong Higher Education Institutes, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, People's Republic of China.,Laboratory of Developmental Biology and Regenerative Medicine, School of Medicine, South China University of Technology, Guangzhou 510006, People's Republic of China
| | - Yiyue Zhang
- Key Laboratory of Zebrafish Modeling and Drug Screening for Human Diseases of Guangdong Higher Education Institutes, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, People's Republic of China
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Kim JE, Lee YM, Lee JH, Noh JK, Kim HC, Park CJ, Park JW, Kim KK. Development and Validation of Single Nucleotide Polymorphism (SNP) Markers from an Expressed Sequence Tag (EST) Database in Olive Flounder (Paralichthys olivaceus). Dev Reprod 2015; 18:275-86. [PMID: 25949198 DOI: 10.12717/devrep.2014.18.4.275] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Revised: 12/05/2014] [Accepted: 12/08/2014] [Indexed: 12/24/2022]
Abstract
To successful molecular breeding, identification and functional characterization of breeding related genes and development of molecular breeding techniques using DNA markers are essential. Although the development of a useful marker is difficult in the aspect of time, cost and effort, many markers are being developed to be used in molecular breeding and developed markers have been used in many fields. Single nucleotide polymorphisms (SNPs) markers were widely used for genomic research and breeding, but has hardly been validated for screening functional genes in olive flounder. We identified single nucleotide polymorphisms (SNPs) from expressed sequence tag (EST) database in olive flounder; out of a total 4,327 ESTs, 693 contigs and 514 SNPs were detected in total EST, and these substitutions include 297 transitions and 217 transversions. As a result, 144 SNP markers were developed on the basis of 514 SNP to selection of useful gene region, and then applied to each of eight wild and culture olive flounder (total 16 samples). In our experimental result, only 32 markers had detected polymorphism in sample, also identified 21 transitions and 11 transversions, whereas indel was not detected in polymorphic SNPs. Heterozygosity of wild and cultured olive flounder using the 32 SNP markers is 0.34 and 0.29, respectively. In conclusion, we identified SNP and polymorphism in olive flounder using newly designed marker, it supports that developed markers are suitable for SNP detection and diversity analysis in olive flounder. The outcome of this study can be basic data for researches for immunity gene and characteristic with SNP.
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Affiliation(s)
- Jung Eun Kim
- Genetics and Breeding Research Center, NFRDI, Geoje 656-842, Korea
| | - Young Mee Lee
- Genetics and Breeding Research Center, NFRDI, Geoje 656-842, Korea
| | - Jeong-Ho Lee
- Genetics and Breeding Research Center, NFRDI, Geoje 656-842, Korea
| | - Jae Koo Noh
- Genetics and Breeding Research Center, NFRDI, Geoje 656-842, Korea
| | - Hyun Chul Kim
- Genetics and Breeding Research Center, NFRDI, Geoje 656-842, Korea
| | - Choul-Ji Park
- Genetics and Breeding Research Center, NFRDI, Geoje 656-842, Korea
| | - Jong-Won Park
- Genetics and Breeding Research Center, NFRDI, Geoje 656-842, Korea
| | - Kyung-Kil Kim
- Genetics and Breeding Research Center, NFRDI, Geoje 656-842, Korea
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7
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Local adaptation of Gymnocypris przewalskii (Cyprinidae) on the Tibetan Plateau. Sci Rep 2015; 5:9780. [PMID: 25944748 PMCID: PMC4421831 DOI: 10.1038/srep09780] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 03/05/2015] [Indexed: 12/28/2022] Open
Abstract
Divergent selection among environments affects species distributions and can lead to speciation. In this article, we investigated the transcriptomes of two ecotypes of scaleless carp (Gymnocypris przewalskii przewalskii and G. p. ganzihonensis) from the Tibetan Plateau. We used a transcriptome sequencing approach to screen approximately 250,000 expressed sequence tags (ESTs) from the gill and kidney tissues of twelve individuals from the Ganzi River and Lake Qinghai to understand how this freshwater fish has adapted to an ecological niche shift from saline to freshwater. We identified 9,429 loci in the gill transcriptome and 12,034 loci in the kidney transcriptome with significant differences in their expression, of which 242 protein-coding genes exhibited strong positive selection (Ka/Ks > 1). Many of the genes are involved in ion channel functions (e.g., Ca2+-binding proteins), immune responses (e.g., nephrosin) or cellular water absorption functions (e.g., aquaporins). These results have potentially broad importance in understanding shifts from saline to freshwater habitats. Furthermore, this study provides the first transcriptome of G. przewalskii, which will facilitate future ecological genomics studies and aid in the identification of genes underlying adaptation and incipient ecological speciation.
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Andreeva AM, Lamas NE, Serebryakova MV, Ryabtseva IP, Bolshakov VV. Reorganization of low-molecular-weight fraction of plasma proteins in the annual cycle of cyprinidae. BIOCHEMISTRY (MOSCOW) 2015; 80:208-18. [PMID: 25756535 DOI: 10.1134/s0006297915020078] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Reorganization of the low-molecular-weight fraction of cyprinid plasma was analyzed using various electrophoretic techniques (disc electrophoresis, electrophoresis in polyacrylamide concentration gradient, in polyacrylamide with urea, and in SDS-polyacrylamide). The study revealed coordinated changes in the low-molecular-weight protein fractions with seasonal dynamics and related reproductive rhythms of fishes. We used cultured species of the Cyprinidae family with sequenced genomes for the detection of these interrelations in fresh-water and anadromous cyprinid species. The common features of organization of fish low-molecular-weight plasma protein fractions made it possible to make reliable identification of their proteins. MALDI mass-spectrometry analysis revealed the presence of the same proteins (hemopexin, apolipoproteins, and serpins) in the low-molecular-weight plasma fraction in wild species and cultured species with sequenced genomes (carp, zebrafish). It is found that the proteins of the first two classes are organized as complexes made of protein oligomers. Stoichiometry of these complexes changes in concordance with the seasonal and reproductive rhythms.
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Affiliation(s)
- A M Andreeva
- Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok, 152742, Russia.
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9
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Gotesman M, Soliman H, El-Matbouli M. Antibody screening identifies 78 putative host proteins involved in Cyprinid herpesvirus 3 infection or propagation in common carp, Cyprinus carpio L. JOURNAL OF FISH DISEASES 2013; 36:721-33. [PMID: 23347276 PMCID: PMC3961710 DOI: 10.1111/jfd.12073] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Revised: 11/16/2012] [Accepted: 11/17/2012] [Indexed: 05/15/2023]
Abstract
Cyprinid herpesvirus 3 (CyHV-3) is the aetiological agent of a serious and notifiable disease afflicting common and koi carp, Cyprinus carpio L., termed koi herpesvirus disease (KHVD). Significant progress has been achieved in the last 15 years, since the initial reports surfaced from Germany, USA and Israel of the CyHV-3 virus, in terms of pathology and detection. However, relatively few studies have been carried out in understanding viral replication and propagation. Antibody-based affinity has been used for detection of CyHV-3 in enzyme-linked immunosorbent assay and PCR-based techniques, and immunohistological assays have been used to describe a CyHV-3 membrane protein, termed ORF81. In this study, monoclonal antibodies linked to N-hydroxysuccinimide (NHS)-activated spin columns were used to purify CyHV-3 and host proteins from tissue samples originating in either CyHV-3 symptomatic or asymptomatic fish. The samples were next analysed either by polyacrylamide gel electrophoresis (PAGE) and subsequently by electrospray ionization coupled to mass spectrometry (ESI-MS) or by ESI-MS analysis directly after purification. A total of 78 host proteins and five CyHV-3 proteins were identified in the two analyses. These data can be used to develop novel control methods for CyHV-3, based on pathways or proteins identified in this study.
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Affiliation(s)
- M Gotesman
- Clinical Division of Fish Medicine, University of Veterinary Medicine, Vienna, Austria
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10
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Hedrich J, Lottaz D, Meyer K, Yiallouros I, Jahnen-Dechent W, Stöcker W, Becker-Pauly C. Fetuin-A and Cystatin C Are Endogenous Inhibitors of Human Meprin Metalloproteases. Biochemistry 2010; 49:8599-607. [DOI: 10.1021/bi1004238] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Jana Hedrich
- Institute of Zoology, Cell and Matrix Biology, Johannes Gutenberg-University, Johannes-von-Müller-Weg 6, 55128 Mainz, Germany
| | - Daniel Lottaz
- Department of Rheumatology, Clinical Immunology and Allergology Inselspital, University of Bern, 3010 Bern, Switzerland
| | - Katharina Meyer
- Institute of Zoology, Cell and Matrix Biology, Johannes Gutenberg-University, Johannes-von-Müller-Weg 6, 55128 Mainz, Germany
| | - Irene Yiallouros
- Institute of Zoology, Cell and Matrix Biology, Johannes Gutenberg-University, Johannes-von-Müller-Weg 6, 55128 Mainz, Germany
| | - Willi Jahnen-Dechent
- Department of Biomedical Engineering, Biointerface Laboratory, RWTH Aachen University, Pauwelsstrasse 30, 52074 Aachen, Germany
| | - Walter Stöcker
- Institute of Zoology, Cell and Matrix Biology, Johannes Gutenberg-University, Johannes-von-Müller-Weg 6, 55128 Mainz, Germany
| | - Christoph Becker-Pauly
- Institute of Zoology, Cell and Matrix Biology, Johannes Gutenberg-University, Johannes-von-Müller-Weg 6, 55128 Mainz, Germany
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Aoki N, Deshimaru M, Kihara K, Terada S. Snake fetuin: Isolation and structural analysis of new fetuin family proteins from the sera of venomous snakes. Toxicon 2009; 54:481-90. [DOI: 10.1016/j.toxicon.2009.05.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2008] [Revised: 05/15/2009] [Accepted: 05/19/2009] [Indexed: 10/20/2022]
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Kirchner S, McDaniel NK, Sugiura SH, Soteropoulos P, Tian B, Fletcher JW, Ferraris RP. Salmonid microarrays identify intestinal genes that reliably monitor P deficiency in rainbow trout aquaculture. Anim Genet 2007; 38:319-31. [PMID: 17596124 DOI: 10.1111/j.1365-2052.2007.01615.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nutrient-responsive genes can identify important metabolic pathways and evaluate optimal dietary levels. Using a 16K Salmo salar microarray, we identified in rainbow trout (Oncorhynchus mykiss) 21 potential phosphorus (P)-responsive genes, mainly involved in immune response, proteolysis or transport, whose expression levels changed in the intestine after 5 days of feeding a low-P (LP) diet. Diet-induced changes in the expression levels of several genes in each fish were tightly correlated with changes in serum P, and the changes persisted for an additional 15 days after dietary P deficiency. We then evaluated these and previously identified P-responsive genes under simulated farm conditions, and monitored the intestinal gene expression from 6 h to 7 days after the trout were switched from a sufficient-P (SP) diet to a LP diet (SP-->LP), and from a LP diet to a SP diet (LP-->SP). After 7 days, mean serum P decreased 0.14 mM/day for SP-->LP and increased 0.10 mm/day for LP-->SP. The mRNA abundance of the metalloendopeptidase meprin 1alpha (MEP1alpha), the Na(+)-dependent phosphate co-transporter (NaPi2b,SLC34A2), the sulfotransferase SULT2beta1 and carbonic anhydrase XIII genes all increased after SP-->LP and decreased after LP-->SP, suggesting that adaptive expression is reversible and correlated with dietary P. The duration of change in gene expression in response to SP-->LP was generally shorter than that of LP-->SP, suggesting potentially different mechanisms of adaptation to deficiency as opposed to excess. Diet-induced changes in mRNA abundance of other genes were either transient or modest. We identified, by heterologous microarray hybridization, new genes sensitive to perturbations in dietary P, and then showed that these genes can reliably monitor P deficiency under field conditions. Simultaneous changes in the expression of these P biomarkers could predict either P deficiency (to prevent economic losses to the farmers) or P excess (to prevent inadvertent pollution of nearby waters).
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Affiliation(s)
- S Kirchner
- Department of Pharmacology and Physiology, University of Medicine and Dentistry of New Jersey (UMDNJ), New Jersey Medical School, Newark, NJ 07103-2714, USA
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Boutet I, Long Ky CL, Bonhomme F. A transcriptomic approach of salinity response in the euryhaline teleost, Dicentrarchus labrax. Gene 2006; 379:40-50. [PMID: 16737785 DOI: 10.1016/j.gene.2006.04.011] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2005] [Revised: 04/11/2006] [Accepted: 04/17/2006] [Indexed: 11/23/2022]
Abstract
Euryhaline teleosts possess the capacity to osmoregulate under various environmental conditions (freshwater to hypersaline water). This physiological capacity is generally monitored using enzyme activity assays (Na+/K+ -ATPase...), hormones quantification (prolactine, growth hormone) or their mRNAs expression. To date, few studies addressed the genetic correlates of adaptation to varying salinity at a molecular level in such fish. In the sea bass Dicentrarchus labrax, genetic differentiation was observed at specific allozyme loci between lagoon- and open-sea populations. In the present study, we investigated transcriptomic response of D. labrax to salt- and freshwater acclimation in two organs involved in osmoregulation, gill and intestine. By using suppression subtractive hybridisation, we characterised 586 partial cDNA sequences encoding proteins potentially involved in the metabolism of sea bass acclimated to salt- or freshwater under experimental conditions. Using these results, we first characterised complete genomic sequence of a carbonic anhydrase and then analysed mRNA expression of genes potentially involved in osmoregulation mechanisms (Na+/K+ -ATPase, carbonic anhydrase, angiotensin-converting enzyme and claudin-3), cell-cycle regulation (secretagogin) and immune system (nephrosin) in gill and intestine of wild fish from open sea and lagoons. Our analyses indicate a strong tissue- and environmental-dependant expression pattern for all the genes studied. A transcriptomic approach such as described in the present paper provides thus a first description of genes involved in metabolic or structural functions important for coping with environmental salinity variations in a euryhaline fish like the common sea bass D. labrax. It should be supplemented by proteomics to check the direct involvement of the gene products at the protein level, and by polymorphism analyses if one is to understand population or individual fluctuations in acclimation to salinity variation.
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Affiliation(s)
- I Boutet
- UMR CNRS-IFREMER 5171 Génome, Populations, Interactions, Adaptation, Station Méditerranéenne de l'Environnement Littoral, 1 Quai de la Daurade, 34200 Sète, France.
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