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Bulat T, Smidak R, Sialana FJ, Jung G, Rattei T, Bilban M, Sattmann H, Lubec G, Aradska J. Transcriptomic and Proteomic Analysis of Arion vulgaris--Proteins for Probably Successful Survival Strategies? PLoS One 2016; 11:e0150614. [PMID: 26986963 PMCID: PMC4795696 DOI: 10.1371/journal.pone.0150614] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 02/17/2016] [Indexed: 11/18/2022] Open
Abstract
The Spanish slug, Arion vulgaris, is considered one of the hundred most invasive species in Central Europe. The immense and very successful adaptation and spreading of A. vulgaris suggest that it developed highly effective mechanisms to deal with infections and natural predators. Current transcriptomic and proteomic studies on gastropods have been restricted mainly to marine and freshwater gastropods. No transcriptomic or proteomic study on A. vulgaris has been carried out so far, and in the current study, the first transcriptomic database from adult specimen of A. vulgaris is reported. To facilitate and enable proteomics in this non-model organism, a mRNA-derived protein database was constructed for protein identification. A gel-based proteomic approach was used to obtain the first generation of a comprehensive slug mantle proteome. A total of 2128 proteins were unambiguously identified; 48 proteins represent novel proteins with no significant homology in NCBI non-redundant database. Combined transcriptomic and proteomic analysis revealed an extensive repertoire of novel proteins with a role in innate immunity including many associated pattern recognition, effector proteins and cytokine-like proteins. The number and diversity in gene families encoding lectins point to a complex defense system, probably as a result of adaptation to a pathogen-rich environment. These results are providing a fundamental and important resource for subsequent studies on molluscs as well as for putative antimicrobial compounds for drug discovery and biomedical applications.
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Affiliation(s)
- Tanja Bulat
- Department of Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Roman Smidak
- Department of Pediatrics, Medical University of Vienna, Vienna, Austria
| | | | - Gangsoo Jung
- Department of Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Thomas Rattei
- Division of Computational System Biology, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Martin Bilban
- Department of Laboratory Medicine and Core Facility Genomics, Medical University of Vienna, Vienna, Austria
| | - Helmut Sattmann
- Third Zoological Department, Museum of Natural History Vienna, Vienna, Austria
| | - Gert Lubec
- Department of Pharmaceutical Chemistry, University of Vienna, Vienna, Austria
- * E-mail: (GL); (JA)
| | - Jana Aradska
- Department of Pediatrics, Medical University of Vienna, Vienna, Austria
- * E-mail: (GL); (JA)
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Dong Y, Dai F, Ren Y, Liu H, Chen L, Yang P, Liu Y, Li X, Wang W, Xiang H. Comparative transcriptome analyses on silk glands of six silkmoths imply the genetic basis of silk structure and coloration. BMC Genomics 2015; 16:203. [PMID: 25886738 PMCID: PMC4372302 DOI: 10.1186/s12864-015-1420-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Accepted: 02/28/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Silk has numerous unique properties that make it a staple of textile manufacturing for several thousand years. However, wider applications of silk in modern have been stalled due to limitations of traditional silk produced by Bombyx mori. While silk is commonly produced by B. mori, several wild non-mulberry silkmoths--especially members of family Saturniidae--produce silk with superior properties that may be useful for wider applications. Further utilization of such silks is hampered by the non-domestication status or limited culturing population of wild silkworms. To date there is insufficient basic genomic or transcriptomic data on these organisms or their silk production. RESULTS We sequenced and compared the transcriptomes of silk glands of six Saturniidae wild silkmoth species through next-generation sequencing technology, identifying 37758 ~ 51734 silkmoth unigenes, at least 36.3% of which are annotated with an e-value less than 10(-5). Sequence analyses of these unigenes identified a batch of genes specific to Saturniidae that are enriched in growth and development. Analyses of silk proteins including fibroin and sericin indicate intra-genus conservation and inter-genus diversification of silk protein features among the wild silkmoths, e.g., isoelectric points, hydrophilicity profile and amino acid composition in motifs of silk H-fibroin. Interestingly, we identified p25 in two of the silkmoths, which were previously predicted to be absent in Saturniidae. There are rapid evolutionary changes in sericin proteins, which might account for the highly heterogeneity of sericin in Saturniidae silkmoths. Within the six sikmoths, both colored-cocoon silkmoth specific transcripts and differentially expressed genes between the colored-cocoon and non-colored-cocoon silkmoths are significantly enriched in catalytic activity, especially transferase activity, suggesting potentially viable targets for future gene mining or genetic manipulation. CONCLUSIONS Our results characterize novel and potentially valuable gene resources of saturniid silkmoths that may facilitate future genetic improvement and modification of mulberry silkworms. Our results suggest that the disparate features of silk--coloration, retention, strength, etc. --are likely not only due to silk proteins, but also to the environment of silk assembly, and more specifically, that stable silk coloration exhibited by some Saturniidae silkmoths may be attributable to active catalytic progress in pigmentation.
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Affiliation(s)
- Yang Dong
- Kunming University of Science and Technology, 727 South Jingming Road, Chenggong District, Kunming, Yunnan Province, 650500, China.,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 East Jiaochang Road, Kunming, Yunnan Province, 650223, China
| | - Fangyin Dai
- State Key Laboratory of Silkworm Genome Biology, Key Sericultural Laboratory of Agricultural Ministry, Institute of Sericulture and Systems Biology, Southwest University, 2 Tiansheng Road, Beibei District, Chongqing, 400715, China
| | - Yandong Ren
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 East Jiaochang Road, Kunming, Yunnan Province, 650223, China
| | - Hui Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 East Jiaochang Road, Kunming, Yunnan Province, 650223, China
| | - Lei Chen
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 East Jiaochang Road, Kunming, Yunnan Province, 650223, China
| | - Pengcheng Yang
- Institute of Zoology, Chinese Academy of Sciences, 69 East Beichen Road, Chaoyang District, Beijing, 100101, China
| | - Yanqun Liu
- Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang Province, 110866, China
| | - Xin Li
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205, USA
| | - Wen Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 East Jiaochang Road, Kunming, Yunnan Province, 650223, China.
| | - Hui Xiang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 East Jiaochang Road, Kunming, Yunnan Province, 650223, China.
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Tsikas D, Duncan MW. Mass spectrometry and 3-nitrotyrosine: strategies, controversies, and our current perspective. MASS SPECTROMETRY REVIEWS 2014; 33:237-76. [PMID: 24167057 DOI: 10.1002/mas.21396] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Revised: 06/24/2013] [Accepted: 06/24/2013] [Indexed: 05/11/2023]
Abstract
Reactive-nitrogen species (RNS) such as peroxynitrite (ONOO(-)), that is, the reaction product of nitric oxide ((•)NO) and superoxide (O2(-•)), nitryl chloride (NO2Cl) and (•)NO2 react with the activated aromatic ring of tyrosine to form 3-nitrotyrosine. This modification, which has been known for more than a century, occurs to both the free form of the amino acid (i.e., soluble/free tyrosine) and to tyrosine residues covalently bound within the backbone of peptides and proteins. Nitration of tyrosine is thought to be of biological significance and has been linked to health and disease, but determining its role has proved challenging. Several key questions have been the focus of much of the research activity: (a) to what extent is free/soluble tyrosine nitrated in biological tissues and fluids, and (b) are there specific site(s) of nitration within peptides/proteins and to what extent (i.e., stoichiometry) does this modification occur? These issues have been addressed in a wide range of sample types (e.g., blood, urine, CSF, exhaled breath condensate and various tissues) and a diverse array of physiological/pathophysiological scenarios. The accurate determination of nitrated tyrosine is, however, a stumbling block. Despite extensive study, the extent to which nitration occurs in vivo, the specificity of the nitration reaction, and its importance in health and disease, remain unclear. In this review, we highlight the analytical challenges and discuss the approaches adopted to address them. Mass spectrometry, in combination with either gas chromatography (GC-MS, GC-MS/MS) or liquid chromatography (LC-MS/MS), has played the central role in the analysis of 3-nitrotyrosine and tyrosine-nitrated biological macromolecules. We discuss its unique attributes and highlight the role of stable-isotope labeled 3-nitrotyrosine analogs in both accurate quantification, and in helping to define the biological relevance of tyrosine nitration. We show that the application of sophisticated mass spectrometric techniques is advantageous if not essential, but that this alone is by no means a guarantee of accurate findings. We discuss the important analytical challenges in quantifying 3-nitrotyrosine, possible workarounds, and we attempt to make sense of the disparate findings that have been reported so far.
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Affiliation(s)
- Dimitrios Tsikas
- Institute of Clinical Pharmacology, Hannover Medical School, Hannover, Germany
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Peptide toxin glacontryphan-M is present in the wings of the butterfly Hebomoia glaucippe (Linnaeus, 1758) (Lepidoptera: Pieridae). Proc Natl Acad Sci U S A 2012; 109:17920-4. [PMID: 23071323 DOI: 10.1073/pnas.1209632109] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Protein profiling has revealed the presence of glacontryphan-M, a peptide toxin identified only in the sea snail genus Conus, in the wings of Hebomoia glaucippe (HG). The wings and body of HG were homogenized and the proteins were extracted and analyzed by 2D gel electrophoresis with subsequent in-gel digestion. Posttranslational protein modifications were detected and analyzed by nano-LC-MS/MS. An antibody was generated against glacontryphan-M, and protein extracts from the wings of HG samples from Malaysia, Indonesia, and the Philippines were tested by immunoblotting. Glacontryphan-M was unambiguously identified in the wings of HG containing the following posttranslational protein modifications: monoglutamylation at E55, methylation at E53, quinone modification at W61, cyanylation at C56, and amidation of the C terminus at G63. Immunoblotting revealed the presence of the toxin in the wings of HG from all origins, showing a single band for glacontryphan-M in HG samples from Malaysia and Philippines and a double band in HG samples from Indonesia. Intriguingly, sequence analysis indicated that the Conus glacontryphan is identical to that of HG. The toxin may function as a defense against diverse predators, including ants, mantes, spiders, lizards, green frogs, and birds.
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