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Wu W, Fields L, DeLaney K, Buchberger AR, Li L. An Updated Guide to the Identification, Quantitation, and Imaging of the Crustacean Neuropeptidome. Methods Mol Biol 2024; 2758:255-289. [PMID: 38549019 DOI: 10.1007/978-1-0716-3646-6_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/02/2024]
Abstract
Crustaceans serve as a useful, simplified model for studying peptides and neuromodulation, as they contain numerous neuropeptide homologs to mammals and enable electrophysiological studies at the single-cell and neural circuit levels. Crustaceans contain well-defined neural networks, including the stomatogastric ganglion, oesophageal ganglion, commissural ganglia, and several neuropeptide-rich organs such as the brain, pericardial organs, and sinus glands. As existing mass spectrometry (MS) methods are not readily amenable to neuropeptide studies, there is a great need for optimized sample preparation, data acquisition, and data analysis methods. Herein, we present a general workflow and detailed methods for MS-based neuropeptidomic analysis of crustacean tissue samples and circulating fluids. In conjunction with profiling, quantitation can also be performed with isotopic or isobaric labeling. Information regarding the localization patterns and changes of peptides can be studied via mass spectrometry imaging. Combining these sample preparation strategies and MS analytical techniques allows for a multi-faceted approach to obtaining deep knowledge of crustacean peptidergic signaling pathways.
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Affiliation(s)
- Wenxin Wu
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Lauren Fields
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Kellen DeLaney
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA.
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, USA.
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2
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Hewadikaram M, Bathige S, Karunaratne V. Dataset of De novo leaf, salicylic induced leaf and flower transcriptome profiling of Datura metel plant. Data Brief 2023; 51:109737. [PMID: 38020423 PMCID: PMC10661695 DOI: 10.1016/j.dib.2023.109737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/19/2023] [Accepted: 10/24/2023] [Indexed: 12/01/2023] Open
Abstract
Datura metel L (thorn's apple) is a popular plant belonging to the family Solanaceae, growing all around the year in humid and warm climates. The importance of D. metel as a medicinal marvel is due to secondary metabolites within various parts of the plant, which serve different therapeutic functions. The whole plant is considered a narcotic, anodyne, and antispasmodic, while the leaves, bark, and seeds are also separately used in extractions. The biological potency of the plant has been used in traditional medicine for over a century. Currently, plant parts are used as a rich source in pharmaceutical manufacturing of secondary metabolites such as flavonoids, saponins, alkaloids, steroids, tannins, and withanaloids. D. metel has proven advanced functions of antiviral effects, antibacterial and antifungal effects, anti-inflammatory, analgesic, antipyretic, hepatoprotective, nephroprotective effect, anticancer, and to treat chronic cardiovascular diseases, diabetes, and neurological ailments. This is the first report on transcriptome assembly for this plant. The raw RNA sequencing data for leaf, salicylic-induced leaf, and flower are available at the NCBI Sequence Read Archive (SRA) under the Bioproject access PRJNA838784. The raw RNA sequencing data that is currently accessible can be utilized to conduct differential gene expression investigations pertaining to various secondary metabolite pathways and diverse tissues, as well as for the research of gene expression related to stress induced by salicylic acid in leaf tissues of the plant. Gene functions can be evaluated and mostly utilized for gene clustering data analysis, gene characterizations, and the identification of genes involved in linked biological pathways in plant studies.
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Affiliation(s)
- Madhavi Hewadikaram
- NSBM Green University, Pitipana, Homagama, Sri Lanka
- Sri Lanka Institute of Nanotechnology, Nanotechnology and Science Park, Mahenwatte, Pitipana, Homagama 10206, Sri Lanka
| | - S.D.N.K. Bathige
- Sri Lanka Institute of Nanotechnology, Nanotechnology and Science Park, Mahenwatte, Pitipana, Homagama 10206, Sri Lanka
| | - Veranja Karunaratne
- Sri Lanka Institute of Nanotechnology, Nanotechnology and Science Park, Mahenwatte, Pitipana, Homagama 10206, Sri Lanka
- SLTC Research University, Padukka, Sri Lanka
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3
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Kono N. A Guide to Sequencing for Long Repetitive Regions. Methods Mol Biol 2023; 2632:131-46. [PMID: 36781726 DOI: 10.1007/978-1-0716-2996-3_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
Full-length analysis of genes with highly repetitive sequences is challenging in two respects: assembly algorithm and sequencing accuracy. The de Bruijn graph often used in short-read assembly cannot distinguish adjacent repeat units. On the other hand, the accuracy of long reads is not yet high enough to identify each and every repeat unit. In this chapter, I present an example of a strategy to solve these problems and obtain the full length of long repeats by combining the extraction and assembly of repeat units based on overlap-layout-consensus and scaffolding by long reads.
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4
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Redin D. Low-Cost Genome-Scale Phasing with Barcode-Linked Sequencing. Methods Mol Biol 2023; 2590:85-99. [PMID: 36335494 DOI: 10.1007/978-1-0716-2819-5_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Complete comprehension of clinically relevant variation among human genomes is likely only to come from sequencing platforms that are cost-efficient, and which feature both accurate base calling and long-range DNA phasing capability. The NGS revolution has struggled to meet the latter of these needs. Here we describe a protocol to address this limitation by preserving the molecular origin of short sequencing reads with an insignificant increase to sequencing costs. Whole haplotype-resolved genomes with megabase-scale phase blocks can be obtained with this method; offering researchers a unique opportunity to tackle the hurdles of de novo sequencing without being limited by a lack of resources.
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Affiliation(s)
- David Redin
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Gene Technology, Science for Life Laboratory, Royal Institute of Technology (KTH), Solna, Sweden.
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5
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Zhang W, Yang C, Liu J, Liang Z, Shan Y, Zhang L, Zhang Y. Accurate discrimination of leucine and isoleucine residues by combining continuous digestion with multiple MS 3 spectra integration in protein sequence. Talanta 2022; 249:123666. [PMID: 35717752 DOI: 10.1016/j.talanta.2022.123666] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 06/07/2022] [Accepted: 06/08/2022] [Indexed: 12/26/2022]
Abstract
Protein de novo sequencing based on tandem mass spectrometry is a crucial technology that enables the identification of peptides without searching databases and assembling unknown sequence proteins, especially for monoclonal antibodies (mAbs). However, the discrimination of leucine (Leu) and isoleucine (Ile) residues in the target protein sequence is still challenging. Herein, we developed an accurate method by continuous digestion with MS3-based fragmentation and multiple spectra integration (evaluated by combined verification score, CVS) to distinguish Leu and Ile residues. Continuous digestion promotes the diversity of peptides in order to expose more Leu and Ile at the N-terminal. CVS integrates multiple MS3 spectra to reduce the interference from noise and co-fragmented ions and improve accuracy. This method successfully resolved all 75 Leu/Ile in bovine serum albumin, especially 3 consecutive Leu/Ile. We further applied the method to analyze trastuzumab and 67 out of the 68 Leu/Ile from the light chain and heavy chain were accurately discriminated, demonstrating the great potential in mAbs sequencing.
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Affiliation(s)
- Weijie Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, 116023, China; University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Chao Yang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, 116023, China; University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Jianhui Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, 116023, China
| | - Zhen Liang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, 116023, China
| | - Yichu Shan
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, 116023, China.
| | - Lihua Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, 116023, China.
| | - Yukui Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, 116023, China
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Vanuopadath M, Raveendran D, Nair BG, Nair SS. Venomics and antivenomics of Indian spectacled cobra (Naja naja) from the Western Ghats. Acta Trop 2022; 228:106324. [PMID: 35093326 DOI: 10.1016/j.actatropica.2022.106324] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/17/2022] [Accepted: 01/18/2022] [Indexed: 01/03/2023]
Abstract
Venom proteome profiling of Naja naja from the Western Ghats region in Kerala was achieved through SDS-PAGE and RP-HPLC followed by Q-TOF LC-MS/MS analysis, incorporating PEAKS and Novor assisted de novo sequencing methodologies. A total of 115 proteins distributed across 17 different enzymatic and non-enzymatic venom protein families were identified through conventional and 39 peptides through homology-driven proteomics approaches. Fourteen peptides derived through de novo complements the Mascot data indicating the importance of homology-driven approaches in improving protein sequence information. Among the protein families identified, glutathione peroxidase and endonuclease were reported for the first time in the Indian cobra venom. Immunological cross-reactivity assessed using Indian polyvalent antivenoms suggested that VINS showed better EC50 (2.48 µg/mL) value than that of PSAV (6.04 µg/mL) and Virchow (6.03 µg/mL) antivenoms. Western blotting experiments indicated that all the antivenoms elicited poor binding specificities, especially towards low molecular mass proteins. Second-generation antivenomics studies revealed that VINS antivenom was less efficient to detect many low molecular mass proteins such as three-finger toxins and Kunitz-type serine protease Inhibitors. Taken together, the present study enabled a large-scale characterization of the venom proteome of Naja naja from the Western Ghats and emphasized the need for developing more efficient antivenoms.
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Affiliation(s)
| | - Dileepkumar Raveendran
- Indriyam Biologics Pvt. Ltd., SCTIMST-TIMed, BMT Wing-Poojappura, Thiruvananthapuram 695 012, Kerala, India
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Perera D, Golizeh M, Ndao M. A Procedure for Analyzing the Proteomic Proteomics Profile of Schistosoma mansoni Cercariae. Methods Mol Biol 2020; 2151:75-84. [PMID: 32451997 DOI: 10.1007/978-1-0716-0635-3_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Schistosomiasis is one of the most important helminthic parasitic infections in the world, with over 700 million people at risk of infection. Species of Schistosoma have a complex life cycle involving the infection of freshwater snails before infecting their mammalian definitive host. Taking about 130,000 lives per annum, S. mansoni is the major cause of intestinal schistosomiasis worldwide. Within Biomphalaria glabrata snails, asexual replication of the parasite gives rise to cercariae larvae. Cercariae actively penetrate the host's skin to complete their life cycle and eventually transform into adult worms. If left untreated, intestinal schistosomiasis can lead to peripheral destruction of the portal vein system, gastric hemorrhage from esophageal varices, as well as hepatic failure. Mass spectrometry (MS) is the method of choice for proteomics analysis. The bottom-up proteomics approach-also known as "shotgun proteomics"-typically includes a protein extraction and solubilization step followed by proteolytic digestion and tandem MS (MS/MS) analysis. Proteins are later identified by peptide de novo sequencing upon MS and MS/MS spectra of digest peptides. In this chapter, we introduce an analytical workflow for proteome profiling of S. mansoni cercariae using bottom-up proteomics. The cercariae were isolated and lysed. Proteins were then extracted, enzymatically digested, and subjected to liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis. Proteins were identified using MaxQuant software. Cercariae are the first life stage of the parasite S. mansoni which humans encounter, and conducting proteomic analysis on this life cycle stage can shed light on possible drug or vaccine candidates to help disable the parasite's ability to infect or arm the immune system for parasite clearance.
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Jain RP, Jayaseelan BF, Wilson Alphonse CR, Mahmoud AH, Mohammed OB, Ahmed Almunqedhi BM, Rajaian Pushpabai R. Mass spectrometric identification and denovo sequencing of novel conotoxins from vermivorous cone snail ( Conus inscriptus), and preliminary screening of its venom for biological activities in vitro and in vivo. Saudi J Biol Sci 2021; 28:1582-95. [PMID: 33732044 DOI: 10.1016/j.sjbs.2020.12.032] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 12/15/2020] [Accepted: 12/17/2020] [Indexed: 12/12/2022] Open
Abstract
Venom of Conus inscriptus, a vermivorous cone snail found abundantly in the southern coastal waters was studied to yield conotoxins through proteomic analysis. A total of 37 conotoxins (4 with single disulfide bonds, 20 with two disulfide bonds and 11 three disulfide-bonded peptides) were identified using mass spectrometric analysis. Among them, amino acid sequences of 11 novel conopeptides with one, two and three disulfides belonging to different classes were derived through manual de novo sequencing. Based on the established primary sequence, they were pharmacologically classified into α conotoxins, µ conotoxins and contryphans. Except In1696 all other conopeptides have undergone C-terminal amidation. The natural venom exhibited 50% lethality at 304.82 µg/mL against zebrafish embryo and 130.31 µg/mL against brine shrimp nauplii. The anticonvulsant study of natural venom effectively reduced the locomotor activity against pentylenetetrazole (PTZ) treated zebrafish. This concludes that the venom peptides from Conus inscriptus exhibit potential anticonvulsant function, which leads to the discovery of lead molecules against seizures.
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Samodova D, Hosfield CM, Cramer CN, Giuli MV, Cappellini E, Franciosa G, Rosenblatt MM, Kelstrup CD, Olsen JV. ProAlanase is an Effective Alternative to Trypsin for Proteomics Applications and Disulfide Bond Mapping. Mol Cell Proteomics 2020; 19:2139-2157. [PMID: 33020190 PMCID: PMC7710147 DOI: 10.1074/mcp.tir120.002129] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 09/29/2020] [Indexed: 01/01/2023] Open
Abstract
Trypsin is the protease of choice in bottom-up proteomics. However, its application can be limited by the amino acid composition of target proteins and the pH of the digestion solution. In this study we characterize ProAlanase, a protease from the fungus Aspergillus niger that cleaves primarily on the C-terminal side of proline and alanine residues. ProAlanase achieves high proteolytic activity and specificity when digestion is carried out at acidic pH (1.5) for relatively short (2 h) time periods. To elucidate the potential of ProAlanase in proteomics applications, we conducted a series of investigations comprising comparative multi-enzymatic profiling of a human cell line proteome, histone PTM analysis, ancient bone protein identification, phosphosite mapping and de novo sequencing of a proline-rich protein and disulfide bond mapping in mAb. The results demonstrate that ProAlanase is highly suitable for proteomics analysis of the arginine- and lysine-rich histones, enabling high sequence coverage of multiple histone family members. It also facilitates an efficient digestion of bone collagen thanks to the cleavage at the C terminus of hydroxyproline which is highly prevalent in collagen. This allows to identify complementary proteins in ProAlanase- and trypsin-digested ancient bone samples, as well as to increase sequence coverage of noncollagenous proteins. Moreover, digestion with ProAlanase improves protein sequence coverage and phosphosite localization for the proline-rich protein Notch3 intracellular domain (N3ICD). Furthermore, we achieve a nearly complete coverage of N3ICD protein by de novo sequencing using the combination of ProAlanase and tryptic peptides. Finally, we demonstrate that ProAlanase is efficient in disulfide bond mapping, showing high coverage of disulfide-containing regions in a nonreduced mAb.
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Affiliation(s)
- Diana Samodova
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Maria V Giuli
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Enrico Cappellini
- Evolutionary Genomics SectionGlobe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Giulia Franciosa
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | | | - Christian D Kelstrup
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Jesper V Olsen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark.
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10
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Takan S, Allmer J. DNMSO; an ontology for representing de novo sequencing results from Tandem-MS data. PeerJ 2020; 8:e10216. [PMID: 33150092 PMCID: PMC7585381 DOI: 10.7717/peerj.10216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 09/28/2020] [Indexed: 11/20/2022] Open
Abstract
For the identification and sequencing of proteins, mass spectrometry (MS) has become the tool of choice and, as such, drives proteomics. MS/MS spectra need to be assigned a peptide sequence for which two strategies exist. Either database search or de novo sequencing can be employed to establish peptide spectrum matches. For database search, mzIdentML is the current community standard for data representation. There is no community standard for representing de novo sequencing results, but we previously proposed the de novo markup language (DNML). At the moment, each de novo sequencing solution uses different data representation, complicating downstream data integration, which is crucial since ensemble predictions may be more useful than predictions of a single tool. We here propose the de novo MS Ontology (DNMSO), which can, for example, provide many-to-many mappings between spectra and peptide predictions. Additionally, an application programming interface (API) that supports any file operation necessary for de novo sequencing from spectra input to reading, writing, creating, of the DNMSO format, as well as conversion from many other file formats, has been implemented. This API removes all overhead from the production of de novo sequencing tools and allows developers to concentrate on algorithm development completely. We make the API and formal descriptions of the format freely available at https://github.com/savastakan/dnmso.
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Affiliation(s)
- Savaş Takan
- Department of Computer Engineering, Faculty of Engineering, Izmir Institute of Technology, Izmir, Turkey
| | - Jens Allmer
- Hochschule Ruhr West, University of Applied Sciences, Medical Informatics and Bioinformatics, Institute for Measurement Engineering and Sensor Technology, Mülheim an der Ruhr, Germany
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Akulova VS, Sharov VV, Aksyonova AI, Putintseva YA, Oreshkova NV, Feranchuk SI, Kuzmin DA, Pavlov IN, Litovka YA, Krutovsky KV. De novo sequencing, assembly and functional annotation of Armillaria borealis genome. BMC Genomics 2020; 21:534. [PMID: 32912216 PMCID: PMC7487993 DOI: 10.1186/s12864-020-06964-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 07/29/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Massive forest decline has been observed almost everywhere as a result of negative anthropogenic and climatic effects, which can interact with pests, fungi and other phytopathogens and aggravate their effects. Climatic changes can weaken trees and make fungi, such as Armillaria more destructive. Armillaria borealis (Marxm. & Korhonen) is a fungus from the Physalacriaceae family (Basidiomycota) widely distributed in Eurasia, including Siberia and the Far East. Species from this genus cause the root white rot disease that weakens and often kills woody plants. However, little is known about ecological behavior and genetics of A. borealis. According to field research data, A. borealis is less pathogenic than A. ostoyae, and its aggressive behavior is quite rare. Mainly A. borealis behaves as a secondary pathogen killing trees already weakened by other factors. However, changing environment might cause unpredictable effects in fungus behavior. RESULTS The de novo genome assembly and annotation were performed for the A. borealis species for the first time and presented in this study. The A. borealis genome assembly contained ~ 68 Mbp and was comparable with ~ 60 and ~ 79.5 Mbp for the A. ostoyae and A. mellea genomes, respectively. The N50 for contigs equaled 50,544 bp. Functional annotation analysis revealed 21,969 protein coding genes and provided data for further comparative analysis. Repetitive sequences were also identified. The main focus for further study and comparative analysis will be on the enzymes and regulatory factors associated with pathogenicity. CONCLUSIONS Pathogenic fungi such as Armillaria are currently one of the main problems in forest conservation. A comprehensive study of these species and their pathogenicity is of great importance and needs good genomic resources. The assembled genome of A. borealis presented in this study is of sufficiently good quality for further detailed comparative study on the composition of enzymes in other Armillaria species. There is also a fundamental problem with the identification and classification of species of the Armillaria genus, where the study of repetitive sequences in the genomes of basidiomycetes and their comparative analysis will help us identify more accurately taxonomy of these species and reveal their evolutionary relationships.
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Affiliation(s)
- Vasilina S Akulova
- Laboratory of Forest Genomics, Genome Research and Education Center, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, 660036, Krasnoyarsk, Russia
- Laboratory of Genomic Research and Biotechnology, Federal Research Center "Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences", 660036, Krasnoyarsk, Russia
| | - Vadim V Sharov
- Laboratory of Forest Genomics, Genome Research and Education Center, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, 660036, Krasnoyarsk, Russia
- Laboratory of Genomic Research and Biotechnology, Federal Research Center "Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences", 660036, Krasnoyarsk, Russia
- Department of High Performance Computing, Institute of Space and Information Technologies, Siberian Federal University, 660074, Krasnoyarsk, Russia
| | - Anastasiya I Aksyonova
- Laboratory of Forest Genomics, Genome Research and Education Center, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, 660036, Krasnoyarsk, Russia
| | - Yuliya A Putintseva
- Laboratory of Forest Genomics, Genome Research and Education Center, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, 660036, Krasnoyarsk, Russia
| | - Natalya V Oreshkova
- Laboratory of Forest Genomics, Genome Research and Education Center, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, 660036, Krasnoyarsk, Russia
- Laboratory of Genomic Research and Biotechnology, Federal Research Center "Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences", 660036, Krasnoyarsk, Russia
- Laboratory of Forest Genetics and Selection, V. N. Sukachev Institute of Forest, Siberian Branch of Russian Academy of Sciences, 660036, Krasnoyarsk, Russia
| | - Sergey I Feranchuk
- Laboratory of Forest Genomics, Genome Research and Education Center, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, 660036, Krasnoyarsk, Russia
- Department of Informatics, National Research Technical University, 664074, Irkutsk, Russia
- Limnological Institute, Siberian Branch of Russian Academy of Sciences, 664033, Irkutsk, Russia
| | - Dmitry A Kuzmin
- Laboratory of Forest Genomics, Genome Research and Education Center, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, 660036, Krasnoyarsk, Russia
- Department of High Performance Computing, Institute of Space and Information Technologies, Siberian Federal University, 660074, Krasnoyarsk, Russia
| | - Igor N Pavlov
- Laboratory of Forest Genomics, Genome Research and Education Center, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, 660036, Krasnoyarsk, Russia
- Laboratory of Reforestation, Mycology and Plant Pathology, V. N. Sukachev Institute of Forest, Siberian Branch of Russian Academy of Sciences, 660036, Krasnoyarsk, Russia
- Department of Chemical Technology of Wood and Biotechnology, Reshetnev Siberian State University of Science and Technology, Krasnoyarsk, 660049, Russia
| | - Yulia A Litovka
- Laboratory of Reforestation, Mycology and Plant Pathology, V. N. Sukachev Institute of Forest, Siberian Branch of Russian Academy of Sciences, 660036, Krasnoyarsk, Russia
- Department of Chemical Technology of Wood and Biotechnology, Reshetnev Siberian State University of Science and Technology, Krasnoyarsk, 660049, Russia
| | - Konstantin V Krutovsky
- Laboratory of Forest Genomics, Genome Research and Education Center, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, 660036, Krasnoyarsk, Russia.
- Department of Forest Genetics and Forest Tree Breeding, Georg-August University of Göttingen, 37077, Göttingen, Germany.
- Center for Integrated Breeding Research, George-August University of Göttingen, 37075, Göttingen, Germany.
- Laboratory of Population Genetics, N. I. Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333, Moscow, Russia.
- Department of Ecosystem Science and Management, Texas A&M University, College Station, TX, 77843-2138, USA.
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Wu Y, Hu S, Ma Y, Zhao B, Yang W, Lu Y, Li P, Du S. Novel Pheretima guillelmi-derived antithrombotic protein DPf3: Identification, characterization, in vitro evaluation and antithrombotic mechanisms investigation. Int J Biol Macromol 2020; 154:545-556. [PMID: 32173431 DOI: 10.1016/j.ijbiomac.2020.03.097] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Revised: 03/03/2020] [Accepted: 03/12/2020] [Indexed: 12/27/2022]
Abstract
In this study, the antithrombotic protein, named DPf3, was purified from Pheretima guillelmi by ion-exchange chromatography. The protein pattern of DPf3 was mainly at 26-34 kDa; its two main proteins, DPf3 ID NO.1 and NO.2, were detected to be 36,121.745 Da and 24,485.004 Da consisting of 329 and 241 amino acids, respectively; the full covered protein sequences were consistent with Ac44553_g1_i1_1 and Dc43026_g1_i1_2 in our previous constructed P. guillelmi local database. The secondary structure of DPf3 is the mixture of α-helix (0.19), β-sheet (0.30) and random coil (0.51). DPf3 was predicted to possess a direct effect on fibrin, fibrinogen and plasminogen by protein-protein docking analysis, which was further confirmed by in vitro and ex vivo study. DPf3 was determined to possess antithrombotic ability by showing outstanding direct-hydrolysis ability on fibrin, fibrinogen and blood clot, and slight plasminogen activation activity. DPf3 could significantly prolong APTT and decrease fibrinogen content, indicating that DPf3 exerted antithrombotic activity via the intrinsic and/or common pathway, and the third coagulation phase. By this approach, the functional protein DPf3 was fully revealed and found to confer excellent anticoagulant and thrombolytic activity, and could be developed into a promising antithrombotic agent.
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Affiliation(s)
- Yali Wu
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, 11 Beisanhuandong Road, Chaoyang District, Beijing 100029, China
| | - Shaonan Hu
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, 11 Beisanhuandong Road, Chaoyang District, Beijing 100029, China
| | - Yunnan Ma
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, 11 Beisanhuandong Road, Chaoyang District, Beijing 100029, China
| | - Bo Zhao
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, 11 Beisanhuandong Road, Chaoyang District, Beijing 100029, China
| | - Wanqing Yang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, 11 Beisanhuandong Road, Chaoyang District, Beijing 100029, China
| | - Yang Lu
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, 11 Beisanhuandong Road, Chaoyang District, Beijing 100029, China
| | - Pengyue Li
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, 11 Beisanhuandong Road, Chaoyang District, Beijing 100029, China
| | - Shouying Du
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, 11 Beisanhuandong Road, Chaoyang District, Beijing 100029, China.
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13
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Vanuopadath M, Shaji SK, Raveendran D, Nair BG, Nair SS. Delineating the venom toxin arsenal of Malabar pit viper (Trimeresurus malabaricus) from the Western Ghats of India and evaluating its immunological cross-reactivity and in vitro cytotoxicity. Int J Biol Macromol 2020; 148:1029-1045. [PMID: 31982532 DOI: 10.1016/j.ijbiomac.2020.01.226] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Revised: 01/22/2020] [Accepted: 01/22/2020] [Indexed: 02/07/2023]
Abstract
The venom protein components of Malabar pit viper (Trimeresurus malabaricus) were identified by combining SDS-PAGE and ion-exchange chromatography pre-fractionation techniques with LC-MS/MS incorporating Novor and PEAKS-assisted de novo sequencing strategies. Total 97 proteins that belong to 16 protein families such as L-amino acid oxidase, metalloprotease, serine protease, phospholipase A2, 5'-nucleotidase, C-type lectins/snaclecs and disintegrin were recognized from the venom of a single exemplar species. Of the 97 proteins, eighteen were identified through de novo approaches. Immunological cross-reactivity assessed through ELISA and western blot indicate that the Indian antivenoms binds less effectively to Malabar pit viper venom components compared to that of Russell's viper venom. The in vitro cell viability assays suggest that compared to the normal cells, MPV venom induces concentration dependent cell death in various cancer cells. Moreover, crude venom resulted in chromatin condensation and apoptotic bodies implying the induction of apoptosis. Taken together, the present study enabled in dissecting the venom proteome of Trimeresurus malabaricus and revealed the immuno-cross-reactivity profiles of commercially available Indian polyvalent antivenoms that, in turn, is expected to provide valuable insights on the need in improving antivenom preparations against its bite.
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Affiliation(s)
| | | | - Dileepkumar Raveendran
- Indriyam Biologics Pvt. Ltd., SCTIMST-TIMed, BMT Wing-Poojappura, Thiruvananthapuram 695 012, Kerala, India
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14
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Niu L, Mann M. Quick and clean: Cracking sentences encoded in E. coli by LC-MS/MS, de novo sequencing, and dictionary search. EuPA Open Proteom 2020; 22-23:30-35. [PMID: 31890553 PMCID: PMC6924291 DOI: 10.1016/j.euprot.2019.07.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 07/17/2019] [Indexed: 12/04/2022]
Abstract
In this study, we faced the challenge of deciphering a protein that has been designed and expressed by E. coli in such a way that the amino acid sequence encodes two concatenated English sentences. The letters ‘O’ and ‘U’ in the sentence are both replaced by ‘K’ in the protein. The sequence cannot be found online and carried to-be-discovered modifications. With limited information in hand, to solve the challenge, we developed a workflow consisting of bottom-up proteomics, de novo sequencing and a bioinformatics pipeline for data processing and searching for frequently appearing words. We assembled a complete first question: “Have you ever wondered what the most fundamental limitations in life are?” and validated the result by sequence database search against a customized FASTA file. We also searched the spectra against an E. coli proteome database and found close to 600 endogenous, co-purified E. coli proteins and contaminants introduced during sample handling, which made the inference of the sentence very challenging. We conclude that E. coli can express English sentences, and that de novo sequencing combined with clever sequence database search strategies is a promising tool for the identification of uncharacterized proteins.
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Affiliation(s)
- Lili Niu
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Matthias Mann
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.,Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
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15
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Karunratanakul K, Tang HY, Speicher DW, Chuangsuwanich E, Sriswasdi S. Uncovering Thousands of New Peptides with Sequence-Mask-Search Hybrid De Novo Peptide Sequencing Framework. Mol Cell Proteomics 2019; 18:2478-2491. [PMID: 31591261 PMCID: PMC6885704 DOI: 10.1074/mcp.tir119.001656] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 09/09/2019] [Indexed: 01/03/2023] Open
Abstract
Typical analyses of mass spectrometry data only identify amino acid sequences that exist in reference databases. This restricts the possibility of discovering new peptides such as those that contain uncharacterized mutations or originate from unexpected processing of RNAs and proteins. De novo peptide sequencing approaches address this limitation but often suffer from low accuracy and require extensive validation by experts. Here, we develop SMSNet, a deep learning-based de novo peptide sequencing framework that achieves >95% amino acid accuracy while retaining good identification coverage. Applications of SMSNet on landmark proteomics and peptidomics studies reveal over 10,000 previously uncharacterized HLA antigens and phosphopeptides, and in conjunction with database-search methods, expand the coverage of peptide identification by almost 30%. The power to accurately identify new peptides of SMSNet would make it an invaluable tool for any future proteomics and peptidomics studies, including tumor neoantigen discovery, antibody sequencing, and proteome characterization of non-model organisms.
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Affiliation(s)
- Korrawe Karunratanakul
- Department of Computer Engineering, Faculty of Engineering, Chulalongkorn University, Bangkok 10330, Thailand
| | - Hsin-Yao Tang
- Proteomics and Metabolomics Facility, The Wistar Institute, Philadelphia, PA 19104
| | - David W Speicher
- Center for Systems and Computational Biology, The Wistar Institute, Philadelphia, PA 19104
| | - Ekapol Chuangsuwanich
- Department of Computer Engineering, Faculty of Engineering, Chulalongkorn University, Bangkok 10330, Thailand; Computational Molecular Biology Group, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand. mailto:
| | - Sira Sriswasdi
- Computational Molecular Biology Group, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand; Research Affairs, Faculty of Medicine, Chulalongkorn University and King Chulalongkorn Memorial Hospital, Bangkok 10330, Thailand. mailto:
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16
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Zhang G, Li J, Zhang J, Liang X, Zhang X, Wang T, Yin S. Integrated Analysis of Transcriptomic, miRNA and Proteomic Changes of a Novel Hybrid Yellow Catfish Uncovers Key Roles for miRNAs in Heterosis. Mol Cell Proteomics 2019; 18:1437-1453. [PMID: 31092672 PMCID: PMC6601203 DOI: 10.1074/mcp.ra118.001297] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 04/09/2019] [Indexed: 01/14/2023] Open
Abstract
Heterosis is a complex biological phenomenon in which hybridization produces offspring that exhibit superior phenotypic characteristics compared with the parents. Heterosis is widely utilized in agriculture, for example in fish farming; however, its underlying molecular basis remains elusive. To gain a comprehensive and unbiased molecular understanding of fish heterosis, we analyzed the mRNA, miRNA, and proteomes of the livers of three catfish species, Pelteobagrus fulvidraco, P. vachelli, and their hybrid, the hybrid yellow catfish "Huangyou-1" (P. fulvidraco ♀ × P. vachelli ♂). Using next-generation sequencing and mass spectrometry, we show that the nonadditive, homoeolog expression bias and expression level dominance pattern were readily identified at the transcriptional, post-transcriptional, or protein levels, providing the evidence for the widespread presence of dominant models during hybridization. A number of predicted miRNA-mRNA-protein pairs were found and validated by qRT-PCR and PRM assays. Furthermore, several diverse key pathways were identified, including immune defense, metabolism, digestion and absorption, and cell proliferation and development, suggesting the vital mechanisms involved in the generation of the heterosis phenotype in progenies. We propose that the high parental expression of genes/proteins (growth, nutrition, feeding, and disease resistance) coupled with low parental miRNAs of the offspring, are inherited from the mother or father, thus indicating that the offspring were enriched with the advantages of the father or mother. We provide new and important information about the molecular mechanisms of heterosis, which represents a significant step toward a more complete elucidation of this phenomenon.
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Affiliation(s)
- Guosong Zhang
- From the ‡College of Marine Science and Engineering, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China;; §Key Laboratory for Physiology Biochemistry and Application, School of Agriculture and Bioengineering, Heze University, Heze, Shandong 274015, China
| | - Jie Li
- From the ‡College of Marine Science and Engineering, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China;; ¶Co-Innovation Center for Marine Bio-Industry Technology, Lian Yungang, 222005, China
| | - Jiajia Zhang
- From the ‡College of Marine Science and Engineering, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China;; ¶Co-Innovation Center for Marine Bio-Industry Technology, Lian Yungang, 222005, China
| | - Xia Liang
- §Key Laboratory for Physiology Biochemistry and Application, School of Agriculture and Bioengineering, Heze University, Heze, Shandong 274015, China
| | - Xinyu Zhang
- From the ‡College of Marine Science and Engineering, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China;; ¶Co-Innovation Center for Marine Bio-Industry Technology, Lian Yungang, 222005, China
| | - Tao Wang
- From the ‡College of Marine Science and Engineering, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China;; ¶Co-Innovation Center for Marine Bio-Industry Technology, Lian Yungang, 222005, China
| | - Shaowu Yin
- From the ‡College of Marine Science and Engineering, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China;; ¶Co-Innovation Center for Marine Bio-Industry Technology, Lian Yungang, 222005, China.
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17
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Yang H, Li YC, Zhao MZ, Wu FL, Wang X, Xiao WD, Wang YH, Zhang JL, Wang FQ, Xu F, Zeng WF, Overall CM, He SM, Chi H, Xu P. Precision De Novo Peptide Sequencing Using Mirror Proteases of Ac-LysargiNase and Trypsin for Large-scale Proteomics. Mol Cell Proteomics 2019; 18:773-785. [PMID: 30622160 PMCID: PMC6442358 DOI: 10.1074/mcp.tir118.000918] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Revised: 11/20/2018] [Indexed: 11/06/2022] Open
Abstract
De novo peptide sequencing for large-scale proteomics remains challenging because of the lack of full coverage of ion series in tandem mass spectra. We developed a mirror protease of trypsin, acetylated LysargiNase (Ac-LysargiNase), with superior activity and stability. The mirror spectrum pairs derived from the Ac-LysargiNase and trypsin treated samples can generate full b and y ion series, which provide mutual complementarity of each other, and allow us to develop a novel algorithm, pNovoM, for de novo sequencing. Using pNovoM to sequence peptides of purified proteins, the accuracy of the sequence was close to 100%. More importantly, from a large-scale yeast proteome sample digested with trypsin and Ac-LysargiNase individually, 48% of all tandem mass spectra formed mirror spectrum pairs, 97% of which contained full coverage of ion series, resulting in precision de novo sequencing of full-length peptides by pNovoM. This enabled pNovoM to successfully sequence 21,249 peptides from 3,753 proteins and interpreted 44-152% more spectra than pNovo+ and PEAKS at a 5% FDR at the spectrum level. Moreover, the mirror protease strategy had an obvious advantage in sequencing long peptides. We believe that the combination of mirror protease strategy and pNovoM will be an effective approach for precision de novo sequencing on both single proteins and proteome samples.
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Affiliation(s)
- Hao Yang
- From the ‡Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS; University of Chinese Academy of Sciences; Institute of Computing Technology, CAS, Beijing 100190, China
| | - Yan-Chang Li
- §State Key Laboratory of Proteomics; Beijing Proteome Research Center; National Center for Protein Sciences Beijing; Beijing Institute of Lifeomics, Beijing 102206, China
| | - Ming-Zhi Zhao
- §State Key Laboratory of Proteomics; Beijing Proteome Research Center; National Center for Protein Sciences Beijing; Beijing Institute of Lifeomics, Beijing 102206, China
| | - Fei-Lin Wu
- §State Key Laboratory of Proteomics; Beijing Proteome Research Center; National Center for Protein Sciences Beijing; Beijing Institute of Lifeomics, Beijing 102206, China
| | - Xi Wang
- From the ‡Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS; University of Chinese Academy of Sciences; Institute of Computing Technology, CAS, Beijing 100190, China
| | - Wei-Di Xiao
- §State Key Laboratory of Proteomics; Beijing Proteome Research Center; National Center for Protein Sciences Beijing; Beijing Institute of Lifeomics, Beijing 102206, China
| | - Yi-Hao Wang
- §State Key Laboratory of Proteomics; Beijing Proteome Research Center; National Center for Protein Sciences Beijing; Beijing Institute of Lifeomics, Beijing 102206, China
| | - Jun-Ling Zhang
- §State Key Laboratory of Proteomics; Beijing Proteome Research Center; National Center for Protein Sciences Beijing; Beijing Institute of Lifeomics, Beijing 102206, China
| | - Fu-Qiang Wang
- §State Key Laboratory of Proteomics; Beijing Proteome Research Center; National Center for Protein Sciences Beijing; Beijing Institute of Lifeomics, Beijing 102206, China
| | - Feng Xu
- §State Key Laboratory of Proteomics; Beijing Proteome Research Center; National Center for Protein Sciences Beijing; Beijing Institute of Lifeomics, Beijing 102206, China
| | - Wen-Feng Zeng
- From the ‡Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS; University of Chinese Academy of Sciences; Institute of Computing Technology, CAS, Beijing 100190, China
| | - Christopher M Overall
- ‖Centre for Blood Research, University of British Columbia, Vancouver, British Columbia, Canada
| | - Si-Min He
- From the ‡Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS; University of Chinese Academy of Sciences; Institute of Computing Technology, CAS, Beijing 100190, China;.
| | - Hao Chi
- From the ‡Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS; University of Chinese Academy of Sciences; Institute of Computing Technology, CAS, Beijing 100190, China;.
| | - Ping Xu
- §State Key Laboratory of Proteomics; Beijing Proteome Research Center; National Center for Protein Sciences Beijing; Beijing Institute of Lifeomics, Beijing 102206, China;; ¶Key Laboratory of Combinatorial Biosynthesis and Drug Discovery of Ministry of Education Wuhan University, Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, China;; College of Life Sciences, Hebei University, Baoding 071002, China.
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18
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Indeykina MI, Podgrudkov DA, Kononikhin AS. The author identified by his method: EuPA YPIC challenge solved. EuPA Open Proteom 2018; 20:1-8. [PMID: 30547002 DOI: 10.1016/j.euprot.2018.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2017] [Revised: 10/08/2018] [Accepted: 10/09/2018] [Indexed: 12/04/2022]
Abstract
EuPA YPIC challenge. Synthetic peptides, sequencing, unusual database. De novo MS/MS, PTMs, sequencing/synthesis errors.
Here we present the results of our attempt on the EuPA YPIC challenge. The task was to sequence the provided synthetic peptides, build the sentence encrypted in them and determine from which book the sentence originated. The task itself, while holding no direct scientific value, offers an insight in less formal terms (for participants at least) on how the overall process of a scientific study of a “new protein” looks like. Hence, we decided to look at the challenge as if it was a general task of sequencing an unknown protein from an unusual proteome database. To solve the task we used LC–MS/MS, MALDI-MS and de novo sequencing. A combination of two MS instruments and de novo MS/MS data analysis make it possible to sequence new peptides and proteins not yet present in proteomic databases.
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19
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Diz AP, Romero MR, Pérez-Figueroa A, Swanson WJ, Skibinski DOF. RNA-seq data from mature male gonads of marine mussels Mytilus edulis and M. galloprovincialis. Data Brief 2018; 21:167-175. [PMID: 30364736 PMCID: PMC6197779 DOI: 10.1016/j.dib.2018.09.086] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 09/21/2018] [Accepted: 09/30/2018] [Indexed: 02/01/2023] Open
Abstract
The mussels Mytilus edulis and Mytilus galloprovincialis are marine organisms with external fertilization able to hybridize where their distributions overlap allowing the study of reproductive isolation mechanisms in nature. We provide raw data of a transcriptomic analysis of mature male gonads from these two Mytilus spp. using NGS (Illumina) technology and a preliminary list of transcript that were functionally annotated showing species-specific differential expression. A shortlist including some of these genes and their corresponding proteins have been thoroughly analysed and discussed in Romero et al. (2018, Submitted for publication).
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Affiliation(s)
- Angel P Diz
- Department of Biochemistry, Genetics and Immunology, Faculty of Biology, University of Vigo, Vigo, Spain.,Marine Research Centre, University of Vigo (CIM-UVIGO), Isla de Toralla, Vigo, Spain
| | - Mónica R Romero
- Department of Biochemistry, Genetics and Immunology, Faculty of Biology, University of Vigo, Vigo, Spain.,Marine Research Centre, University of Vigo (CIM-UVIGO), Isla de Toralla, Vigo, Spain
| | - Andrés Pérez-Figueroa
- Department of Biochemistry, Genetics and Immunology, Faculty of Biology, University of Vigo, Vigo, Spain
| | - Willie J Swanson
- Department of Genome Sciences, School of Medicine, University of Washington, Seattle, USA
| | - David O F Skibinski
- Institute of Life Science, Swansea University Medical School, Swansea University, Swansea, UK
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20
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Zhang H, Fu Y, Wang L, Liang A, Chen S, Xu A. Identifying novel conopepetides from the venom ducts of Conus litteratus through integrating transcriptomics and proteomics. J Proteomics 2018; 192:346-357. [PMID: 30267875 DOI: 10.1016/j.jprot.2018.09.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 09/20/2018] [Accepted: 09/25/2018] [Indexed: 12/17/2022]
Abstract
The venom ducts of marine cone snails secrete highly complex mixtures of cysteine-rich active peptides, which are generally known as conotoxins or conopeptides and provide a potential fertile resource for pharmacological neuroscience research and the discovery of new drugs. Previous studies have devoted substantial effort to the identification of novel conopeptides, and the 109 cone snail species have yielded 7000 known conopeptides to date. Here, we used de novo deep transcriptome sequencing analyses combined with traditional Sanger sequencing and liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS) to identify 30 distinct conopeptide precursors. Twenty of these were previously reported and the other 10 were novel conopeptide precursors. The study provides the first identification of the Con-ikot-ikot, NSF-bt05, O3 and I1 gene superfamilies in C. litteratus. A new putative superfamily was identified. In addition, the following cysteine frameworks were first identified in this study: CC-C-C-C-C-C-C-C-C-C-C-C-CC-C-C-C-C-C and C-C-C-C-C-CC-C. Several isomerases involved in post-translational modification of conopeptides were identified as well. The discovery of new conopeptides in C. litteratus will enhance our understanding of the conopeptide diversity in this particular clade of cone snails. We also found the existence of intraspecific variations in vermivorous species. Finally, the analysis strategy offers a relatively reliable workflow for screening for peptide drug candidates. SIGNIFICANCE: These novel conopeptides provide a potential resource for the development of new channel-targeting drugs. The intraspecific variation in C. litteratus enhance our understanding of the conopeptide diversity in this particular clade of cone snails. The identified three cysteine residues, which might participate in the formation of disulfide bonds, provide a clue to get the connectivity of cysteine frameworks. Finally, the analysis strategy offers a relatively reliable workflow for screening for peptide drug candidates.
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Affiliation(s)
- Han Zhang
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China; Shenzhen Research Institute, Sun Yat-Sen University, People's Republic of China
| | - Yonggui Fu
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China; Shenzhen Research Institute, Sun Yat-Sen University, People's Republic of China
| | - Lei Wang
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China; Shenzhen Research Institute, Sun Yat-Sen University, People's Republic of China
| | - Anwen Liang
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Shangwu Chen
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China; Shenzhen Research Institute, Sun Yat-Sen University, People's Republic of China.
| | - Anlong Xu
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China; School of Life Science, Beijing University of Chinese Medicine, Beijing 100029, People's Republic of China.
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21
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Mylonas R, Beer I, Iseli C, Chong C, Pak HS, Gfeller D, Coukos G, Xenarios I, Müller M, Bassani-Sternberg M. Estimating the Contribution of Proteasomal Spliced Peptides to the HLA-I Ligandome. Mol Cell Proteomics 2018; 17:2347-2357. [PMID: 30171158 PMCID: PMC6283289 DOI: 10.1074/mcp.ra118.000877] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 08/27/2018] [Indexed: 12/21/2022] Open
Abstract
It has been reported that about 30% of the HLA-I ligands are produced by proteasomal splicing of two noncontiguous fragments of a parental protein. We report that the identification of many of those spliced peptides is ambiguous. With an alternative workflow, based on de novo sequencing and subsequent verification with multiple search tools, we estimate that the upper bound for the proportion of cis-spliced peptides is 2–6%. Nevertheless, the true contribution of spliced peptides to the ligandome may be much smaller. Spliced peptides are short protein fragments spliced together in the proteasome by peptide bond formation. True estimation of the contribution of proteasome-spliced peptides (PSPs) to the global human leukocyte antigen (HLA) ligandome is critical. A recent study suggested that PSPs contribute up to 30% of the HLA ligandome. We performed a thorough reanalysis of the reported results using multiple computational tools and various validation steps and concluded that only a fraction of the proposed PSPs passes the quality filters. To better estimate the actual number of PSPs, we present an alternative workflow. We performed de novo sequencing of the HLA-peptide spectra and discarded all de novo sequences found in the UniProt database. We checked whether the remaining de novo sequences could match spliced peptides from human proteins. The spliced sequences were appended to the UniProt fasta file, which was searched by two search tools at a false discovery rate (FDR) of 1%. We find that 2–6% of the HLA ligandome could be explained as spliced protein fragments. The majority of these potential PSPs have good peptide-spectrum match properties and are predicted to bind the respective HLA molecules. However, it remains to be shown how many of these potential PSPs actually originate from proteasomal splicing events.
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Affiliation(s)
- Roman Mylonas
- Vital-IT, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Ilan Beer
- Adicet Bio Israel, Ltd., Technion City, 32000, Haifa, Israel
| | - Christian Iseli
- Vital-IT, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Chloe Chong
- Ludwig Cancer Research Center, University of Lausanne, 1066 Epalinges, Switzerland; Department of Oncology, University Hospital of Lausanne, 1011 Lausanne, Switzerland
| | - Hui-Song Pak
- Ludwig Cancer Research Center, University of Lausanne, 1066 Epalinges, Switzerland; Department of Oncology, University Hospital of Lausanne, 1011 Lausanne, Switzerland
| | - David Gfeller
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland; Ludwig Cancer Research Center, University of Lausanne, 1066 Epalinges, Switzerland
| | - George Coukos
- Ludwig Cancer Research Center, University of Lausanne, 1066 Epalinges, Switzerland; Department of Oncology, University Hospital of Lausanne, 1011 Lausanne, Switzerland
| | - Ioannis Xenarios
- Vital-IT, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Markus Müller
- Vital-IT, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.
| | - Michal Bassani-Sternberg
- Vital-IT, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.
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22
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Barth T, Mandacaru SC, Charneau S, Souza MVD, Ricart CAO, Noronha EF, Souza AA, Freitas SMD, Roepstorff P, Fontes W, Castro MS, Pires Júnior OR. Biochemical and structural characterization of a protein complex containing a hyaluronidase and a CRISP-like protein isolated from the venom of the spider Acanthoscurria natalensis. J Proteomics 2018; 192:102-113. [PMID: 30165259 DOI: 10.1016/j.jprot.2018.08.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 07/23/2018] [Accepted: 08/19/2018] [Indexed: 12/19/2022]
Abstract
Spider venoms are composed of a complex mixture of bioactive molecules. The structural and functional characterization of these molecules in the venom of the Brazilian spider Acanthoscurria natalensis, has been little explored. The venom was fractionated using reversed-phase liquid chromatography. The fraction with hyaluronidase activity was named AnHyal. The partial sequencing of AnHyal revealed the presence of a CRISP-like protein, in addition to hyaluronidase, comprising 67% coverage for hyaluronidase from Brachypelma vagans and 82% for CRISP-like protein from Grammostola rosea. 1D BN-PAGE zymogram assays of AnHyal confirmed the presence of enzymatically active 53 kDa monomer and 124 and 178 kDa oligomers. The decomposition of the complexes by 2D BN/SDS-PAGE zymogram assays showed two subunits, 53 (AnHyalH) and 44 kDa (AnHyalC), with sequence similarity to hyaluronidase and CRISP proteins, respectively. The secondary structure of AnHyal is composed by 36% of α-helix. AnHyal presented maximum activity at pH between 4.0 and 6.0 and 30 and 60 °C, showed specificity to hyaluronic acid substrate and presented a KM of 617.9 μg/mL. Our results showed that hyaluronidase and CRISP proteins can form a complex and the CRISP protein may contribute to the enzymatic activity of AnHyalH.
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Affiliation(s)
- Tania Barth
- Laboratory of Toxinology, Department of Physiological Sciences/IB, University of Brasilia, Brasilia-DF 70910-900, Brazil; Laboratory of Animal Histology, Department of Biological Sciences, State University of Santa Cruz, Ilhéus-Bahia 45662-900, Brazil.
| | - Samuel Coelho Mandacaru
- Laboratory of Protein Chemistry and Biochemistry, Department of Cell Biology/IB, University of Brasilia, Brasilia-DF, Brazil
| | - Sébastien Charneau
- Laboratory of Protein Chemistry and Biochemistry, Department of Cell Biology/IB, University of Brasilia, Brasilia-DF, Brazil.
| | - Marcelo Valle de Souza
- Laboratory of Protein Chemistry and Biochemistry, Department of Cell Biology/IB, University of Brasilia, Brasilia-DF, Brazil.
| | - Carlos André Ornelas Ricart
- Laboratory of Protein Chemistry and Biochemistry, Department of Cell Biology/IB, University of Brasilia, Brasilia-DF, Brazil.
| | - Eliane Ferreira Noronha
- Laboratory of Enzymology, Department of Cellular Biology/IB, University of Brasília, Brasilia-DF 70910-900, Brazil.
| | - Amanda Araújo Souza
- Laboratory of Molecular Biophysics, Department of Cellular Biology/IB, University of Brasília, Brasilia-DF 70910-900, Brazil
| | - Sonia Maria de Freitas
- Laboratory of Molecular Biophysics, Department of Cellular Biology/IB, University of Brasília, Brasilia-DF 70910-900, Brazil.
| | - Peter Roepstorff
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark.
| | - Wagner Fontes
- Laboratory of Protein Chemistry and Biochemistry, Department of Cell Biology/IB, University of Brasilia, Brasilia-DF, Brazil.
| | - Mariana S Castro
- Laboratory of Toxinology, Department of Physiological Sciences/IB, University of Brasilia, Brasilia-DF 70910-900, Brazil; Laboratory of Protein Chemistry and Biochemistry, Department of Cell Biology/IB, University of Brasilia, Brasilia-DF, Brazil.
| | - Osmindo Rodrigues Pires Júnior
- Laboratory of Toxinology, Department of Physiological Sciences/IB, University of Brasilia, Brasilia-DF 70910-900, Brazil.
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Knickelbine JJ, Konop CJ, Viola IR, Rogers CB, Messinger LA, Vestling MM, Stretton AOW. Different Bioactive Neuropeptides are Expressed in Two Sub-Classes of GABAergic RME Nerve Ring Motorneurons in Ascaris suum. ACS Chem Neurosci 2018; 9:2025-2040. [PMID: 29400437 DOI: 10.1021/acschemneuro.7b00450] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Neuropeptides can have significant effects on neurons and synapses, but among the ∼250 predicted peptides in nematodes, few have been characterized functionally. Here, we report new neuropeptides in the 4 RME nerve ring motorneurons of the nematode Ascaris suum. These GABAergic neurons are involved in three-dimensional head movement. Mass spectrometry (MS) of single dissected RMEs detected a total of 12 neuropeptides (encoded by five genes), nine of which are novel. None of these are expressed in the DI/VI inhibitory GABAergic motorneurons that synapse onto body wall muscle. Using peptide sequences obtained by tandem MS, we cloned the peptide-encoding transcripts and synthesized riboprobes for in situ hybridization (ISH). This complementary technique corroborated the results from single-cell MS, showing that the dissections were not contaminated with adhering tissue from other cells. We also synthesized a multiple antigenic peptide to raise a highly specific antibody against one of the endogenous peptides, which labeled the same cells detected by MS and ISH. Our results show that the RMEs can be divided into two subsets: RMED/V (expressing afp-2, afp-15, Asu-nlp-58, and high levels of afp-16) and RMEL/R (expressing afp-15 and low levels of afp-4 and afp-16). Almost all of these peptides are bioactive in A. suum.
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24
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Hong SM, Kwon HJ, Park SJ, Seong WJ, Kim I, Kim JH. Genomic and probiotic characterization of SJP-SNU strain of Pichia kudriavzevii. AMB Express 2018; 8:80. [PMID: 29774473 PMCID: PMC5957016 DOI: 10.1186/s13568-018-0609-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 05/03/2018] [Indexed: 12/30/2022] Open
Abstract
The yeast strain SJP-SNU was investigated as a probiotic and was characterized with respect to growth temperature, bile salt resistance, hydrogen sulfide reducing activity, intestinal survival ability and chicken embryo pathogenicity. In addition, we determined the complete genomic and mitochondrial sequences of SJP-SNU and conducted comparative genomics analyses. SJP-SNU grew rapidly at 37 °C and formed colonies on MacConkey agar containing bile salt. SJP-SNU reduced hydrogen sulfide produced by Salmonella serotype Enteritidis and, after being fed to 4-week-old chickens, could be isolated from cecal feces. SJP-SNU did not cause mortality in 10-day-old chicken embryos. From 13 initial contigs, 11 were finally assembled and represented 10 chromosomal sequences and 1 mitochondrial DNA sequence. Comparative genomic analyses revealed that SJP-SNU was a strain of Pichia kudriavzevii. Although SJP-SNU possesses pathogenicity-related genes, they showed very low amino acid sequence identities to those of Candida albicans. Furthermore, SJP-SNU possessed useful genes, such as phytases and cellulase. Thus, SJP-SNU is a useful yeast possessing the basic traits of a probiotic, and further studies to demonstrate its efficacy as a probiotic in the future may be warranted.
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25
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Kleinnijenhuis AJ, van Holthoon FL. Domain-Specific Proteogenomic Analysis of Collagens to Evaluate De Novo Sequencing Results and Database Information. J Mol Evol 2018; 86:293-302. [PMID: 29721580 DOI: 10.1007/s00239-018-9844-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 04/26/2018] [Indexed: 10/17/2022]
Abstract
Collagen is an important structural protein and the most abundant protein in mammals. In several research fields, structural analysis of collagens is performed. Fibrillar collagens almost entirely consist of continuous repeats of GXY, where G is glycine, X is often proline or alanine and Y is often hydroxyproline or alanine. In the present study, the collagen structure was investigated in detail at the nucleotide, codon group, amino acid and target peptide level using sequence analyses. One of the most important findings was that a selection of codon groups is predominantly involved in amino acid changes between closely related collagens and that other change routes come up when collagens are less related. The findings of the sequence analyses were used to evaluate reported sequences of non-avian dinosaur species and database entries of duck and chicken collagen. The duck assessment was supported by an experimental data set, obtained by collagen extraction from duck skin and subsequent digestion and LC-MS analysis. It was found that database entries of chicken and duck collagen 3α1 contained unreliable features, such as missing parts, no continuous GXY pattern and too many interspecies differences. As an example, the erroneous nature of one of these unreliable features was confirmed experimentally using LC-MS. Finally, dino and bird collagen 1α1 were compared. The presented results will show that performing a domain-specific proteogenomic analysis provides very useful information to assess de novo sequencing results and database information of collagens. Furthermore, it offers deeper insight in the functional restrictions and routes of evolutionary divergence.
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26
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Anapindi KDB, Romanova EV, Southey BR, Sweedler JV. Peptide identifications and false discovery rates using different mass spectrometry platforms. Talanta 2018; 182:456-463. [PMID: 29501178 DOI: 10.1016/j.talanta.2018.01.062] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 01/28/2018] [Indexed: 12/29/2022]
Abstract
Characterization of endogenous neuropeptides produced from post-translational proteolytic processing of precursor proteins is a demanding task. A variety of complex prohormone processing steps generate molecular diversity from neuropeptide prohormones, making in silico neuropeptide discovery difficult. In addition, the wide range of endogenous peptide concentrations as well as significant peptide complexity further challenge the structural characterization of neuropeptides. Liquid chromatography-mass spectrometry (MS), performed in conjunction with bioinformatics, allows for high-throughput characterization of peptides. Mass analyzers and molecular dissociation techniques render specific characteristics to the acquired data and thus, influence the analysis of the MS data using bioinformatic algorithms for follow-up peptide identification. Here we evaluated the efficacy of several distinct peptidomic workflows using two mass spectrometers, the Thermo Orbitrap Fusion Tribrid and Bruker Impact HD UHR-QqTOF, for confident peptide discovery and characterization. We compared the results in several categories, including the numbers of identified peptides, full-length mature neuropeptides among all identifications, and precursor proteins mapped by the identified peptides. We also characterized the peptide false discovery rate (FDR) based on the occurrence of amidation, a known post-translational modification (PTM) that has been shown to require the presence of a C-terminal glycine. Thus, amidation events without a preceding glycine were considered false-positive amidation assignments. We compared the FDR calculated by the search engine used here to the minimum FDR estimated via false amidation assignments. The search engine severely underestimated the rate of false PTM assignments among the identified peptides, regardless of the specific MS platform used.
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Affiliation(s)
- Krishna D B Anapindi
- Department of Chemistry and the Beckman Institute, University of Illinois at Urbana-Champaign, Urbana 61801, IL, USA
| | - Elena V Romanova
- Department of Chemistry and the Beckman Institute, University of Illinois at Urbana-Champaign, Urbana 61801, IL, USA
| | - Bruce R Southey
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana 61801, IL, USA
| | - Jonathan V Sweedler
- Department of Chemistry and the Beckman Institute, University of Illinois at Urbana-Champaign, Urbana 61801, IL, USA.
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Abd El-Aziz TM, Al Khoury S, Jaquillard L, Triquigneaux M, Martinez G, Bourgoin-Voillard S, Sève M, Arnoult C, Beroud R, De Waard M. Actiflagelin, a new sperm activator isolated from Walterinnesia aegyptia venom using phenotypic screening. J Venom Anim Toxins Incl Trop Dis 2018; 24:2. [PMID: 29410678 PMCID: PMC5782387 DOI: 10.1186/s40409-018-0140-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 01/02/2018] [Indexed: 02/07/2023] Open
Abstract
Background Sperm contains a wealth of cell surface receptors and ion channels that are required for most of its basic functions such as motility and acrosome reaction. Conversely, animal venoms are enriched in bioactive compounds that primarily target those ion channels and cell surface receptors. We hypothesized, therefore, that animal venoms should be rich enough in sperm-modulating compounds for a drug discovery program. Our objective was to demonstrate this fact by using a sperm-based phenotypic screening to identify positive modulators from the venom of Walterinnesia aegyptia. Methods Herein, as proof of concept that venoms contain interesting compounds for sperm physiology, we fractionated Walterinnesia aegyptia snake venom by RP-HPLC and screened for bioactive fractions capable of accelerating mouse sperm motility (primary screening). Next, we purified each compound from the positive fraction by cation exchange and identified the bioactive peptide by secondary screening. The peptide sequence was established by Edman sequencing of the reduced/alkylated compound combined to LC-ESI-QTOF MS/MS analyses of reduced/alkylated fragment peptides following trypsin or V8 protease digestion. Results Using this two-step purification protocol combined to cell phenotypic screening, we identified a new toxin of 7329.38 Da (actiflagelin) that activates sperm motility in vitro from OF1 male mice. Actiflagelin is 63 amino acids in length and contains five disulfide bridges along the proposed pattern of disulfide connectivity C1-C5, C2-C3, C4-C6, C7-C8 and C9-C10. Modeling of its structure suggests that it belongs to the family of three finger toxins with a noticeable homology with bucandin, a peptide from Bungarus candidus venom. Conclusions This report demonstrates the feasibility of identifying profertility compounds that may be of therapeutic potential for infertility cases where motility is an issue.
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Affiliation(s)
- Tarek Mohamed Abd El-Aziz
- 1Institute of Thorax, INSERM UMR 1087/CNRS UMR 6291, LabEx Ion Channels, Science and Therapeutics, 8 Quai Moncousu, BP 70721, 44007 Nantes Cedex 1, France.,2University of Nantes, 44007 Nantes, France.,3Zoology Department, Faculty of Science, Minia University, El-Minia, 61519 Egypt
| | - Sawsan Al Khoury
- 1Institute of Thorax, INSERM UMR 1087/CNRS UMR 6291, LabEx Ion Channels, Science and Therapeutics, 8 Quai Moncousu, BP 70721, 44007 Nantes Cedex 1, France.,2University of Nantes, 44007 Nantes, France
| | - Lucie Jaquillard
- Smartox Biotechnology, 570 Rue de la Chimie, 38400 Saint Martin d'Hères, France
| | | | - Guillaume Martinez
- 5University Grenoble Alpes, PROMETHEE proteomic Platform, 38000 Grenoble, France.,INSERM 1209, CNRS UMR 5309, Equipe "Génétique, Epigénétique et Thérapies de l'Infertilité", 38000 Grenoble, France
| | - Sandrine Bourgoin-Voillard
- 5University Grenoble Alpes, PROMETHEE proteomic Platform, 38000 Grenoble, France.,7Institut de Biologie et de Pathologie, CHU de Grenoble, PROMETHEE proteomic Platform, 38000 Grenoble, France.,Inserm U1055, LBFA and BEeSy, Saint Martin d'Hères, France
| | - Michel Sève
- 5University Grenoble Alpes, PROMETHEE proteomic Platform, 38000 Grenoble, France.,7Institut de Biologie et de Pathologie, CHU de Grenoble, PROMETHEE proteomic Platform, 38000 Grenoble, France.,Inserm U1055, LBFA and BEeSy, Saint Martin d'Hères, France
| | - Christophe Arnoult
- 5University Grenoble Alpes, PROMETHEE proteomic Platform, 38000 Grenoble, France.,INSERM 1209, CNRS UMR 5309, Equipe "Génétique, Epigénétique et Thérapies de l'Infertilité", 38000 Grenoble, France
| | - Rémy Beroud
- Smartox Biotechnology, 570 Rue de la Chimie, 38400 Saint Martin d'Hères, France
| | - Michel De Waard
- 1Institute of Thorax, INSERM UMR 1087/CNRS UMR 6291, LabEx Ion Channels, Science and Therapeutics, 8 Quai Moncousu, BP 70721, 44007 Nantes Cedex 1, France.,2University of Nantes, 44007 Nantes, France.,Smartox Biotechnology, 570 Rue de la Chimie, 38400 Saint Martin d'Hères, France
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28
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Peharec Štefanić P, Cindrić M, Balen B. Proteomic Analysis of Non-model Plant Tissues Using Phenol Extraction, Two-Dimensional Electrophoresis, and MALDI Mass Spectrometry. Methods Mol Biol 2018; 1815:351-370. [PMID: 29981135 DOI: 10.1007/978-1-4939-8594-4_25] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Separation of plant proteins by means of electrophoretic techniques is quite challenging since different compounds typical for plant cells can interfere and/or reduce the effectiveness of the protein isolation. This is particularly problematic for two-dimensional electrophoresis (2-DE). Therefore, it is important to optimize protein extraction and to establish a robust protocol for 2-DE and downstream processing, primarily mass spectrometry (MS) analysis. Here we give a detailed protocol for protein extraction using phenol method, 2-DE, and MALDI-MS analysis.
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Affiliation(s)
- Petra Peharec Štefanić
- Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Mario Cindrić
- Division of Molecular Medicine, Ruđer Bošković Institute, Zagreb, Croatia
| | - Biljana Balen
- Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia.
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29
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Abstract
Crustaceans serve as a useful, simplified model for studying peptides and neuromodulation, as they contain numerous neuropeptide homologs to mammals and enable electrophysiological studies at the single-cell and neural circuit levels. In particular, crustaceans contain well-defined neural networks, including the stomatogastric ganglion, esophageal ganglion, commissural ganglia, and several neuropeptide-rich organs, such as the brain, pericardial organs, and sinus glands. Due to the lack of a genomic database for crustacean peptides, an important step of crustacean peptidomics involves the discovery and identification of novel peptides and the construction of a database, more recently with the aid of mass spectrometry (MS). Herein, we present a general workflow and detailed methods for MS-based peptidomic analysis of crustacean tissue samples and circulating fluids. In conjunction with profiling, quantitation can also be performed with isotopic or isobaric labeling. Information regarding the localization patterns and changes of peptides can be studied via mass spectrometry imaging. Combining these sample preparation strategies and MS analytical techniques allows for a multifaceted approach to obtaining deep knowledge of crustacean peptidergic signaling pathways.
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Affiliation(s)
- Kellen DeLaney
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Amanda Buchberger
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA. .,School of Pharmacy, University of Wisconsin-Madison, Madison, WI, USA.
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30
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Kono N, Tomita M, Arakawa K. eRP arrangement: a strategy for assembled genomic contig rearrangement based on replication profiling in bacteria. BMC Genomics 2017; 18:784. [PMID: 29029602 PMCID: PMC5640929 DOI: 10.1186/s12864-017-4162-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 10/05/2017] [Indexed: 12/15/2022] Open
Abstract
Background The reduced cost of sequencing has made de novo sequencing and the assembly of draft microbial genomes feasible in any ordinary biology lab. However, the process of finishing and completing the genome remains labor-intensive and computationally challenging in some cases, such as in the study of complete genome sequences, genomic rearrangements, long-range syntenic relationships, and structural variations. Methods Here, we show a contig reordering strategy based on experimental replication profiling (eRP) to recapitulate the bacterial genome structure within draft genomes. During the exponential growth phase, the majority of bacteria show a global genomic copy number gradient that is enriched near the replication origin and gradually declines toward the terminus. Therefore, if genome sequencing is performed with appropriate timing, the short-read coverage reflects this copy number gradient, providing information about the contig positions relative to the replication origin and terminus. Results We therefore investigated the appropriate timing for genomic DNA sampling and developed an algorithm for the reordering of the contigs based on eRP. As a result, this strategy successfully recapitulates the genomic structure of various structural mutants with draft genome sequencing. Conclusions Our strategy was successful for contig rearrangement with intracellular DNA replication behavior mechanisms and can be applied to almost all bacteria because the DNA replication system is highly conserved. Therefore, eRP makes it possible to understand genomic structural information and long-range syntenic relationships using a draft genome that is based on short reads. Electronic supplementary material The online version of this article (10.1186/s12864-017-4162-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nobuaki Kono
- Institute for Advanced Biosciences, Keio University, Mizukami 246-2, Kakuganji, Tsuruoka, Yamagata, 997-0052, Japan.
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, Mizukami 246-2, Kakuganji, Tsuruoka, Yamagata, 997-0052, Japan
| | - Kazuharu Arakawa
- Institute for Advanced Biosciences, Keio University, Mizukami 246-2, Kakuganji, Tsuruoka, Yamagata, 997-0052, Japan
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31
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Kuchibhotla B, Kola SR, Medicherla JV, Cherukuvada SV, Dhople VM, Nalam MR. Combinatorial Labeling Method for Improving Peptide Fragmentation in Mass Spectrometry. J Am Soc Mass Spectrom 2017; 28:1216-1226. [PMID: 28349438 DOI: 10.1007/s13361-017-1606-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 12/30/2016] [Accepted: 01/09/2017] [Indexed: 06/06/2023]
Abstract
Annotation of peptide sequence from tandem mass spectra constitutes the central step of mass spectrometry-based proteomics. Peptide mass spectra are obtained upon gas-phase fragmentation. Identification of the protein from a set of experimental peptide spectral matches is usually referred as protein inference. Occurrence and intensity of these fragment ions in the MS/MS spectra are dependent on many factors such as amino acid composition, peptide basicity, activation mode, protease, etc. Particularly, chemical derivatizations of peptides were known to alter their fragmentation. In this study, the influence of acetylation, guanidinylation, and their combination on peptide fragmentation was assessed initially on a lipase (LipA) from Bacillus subtilis followed by a bovine six protein mix digest. The dual modification resulted in improved fragment ion occurrence and intensity changes, and this resulted in the equivalent representation of b- and y-type fragment ions in an ion trap MS/MS spectrum. The improved representation has allowed us to accurately annotate the peptide sequences de novo. Dual labeling has significantly reduced the false positive protein identifications in standard bovine six peptide digest. Our study suggests that the combinatorial labeling of peptides is a useful method to validate protein identifications for high confidence protein inference. Graphical Abstract ᅟ.
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Affiliation(s)
- Bhanuramanand Kuchibhotla
- Center for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Uppal Road, Hyderabad, 500007, Telangana, India
| | - Sankara Rao Kola
- Center for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Uppal Road, Hyderabad, 500007, Telangana, India
| | - Jagannadham V Medicherla
- Center for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Uppal Road, Hyderabad, 500007, Telangana, India
| | - Swamy V Cherukuvada
- Center for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Uppal Road, Hyderabad, 500007, Telangana, India
| | - Vishnu M Dhople
- Department of Functional Genomics, University Medicine Greifswald, Interface Institute Genetics & Functional Genomics, D-17475, Greifswald, Germany
| | - Madhusudhana Rao Nalam
- Center for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Uppal Road, Hyderabad, 500007, Telangana, India.
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Saha B, Bhattacharya SG. Charting novel allergens from date palm pollen (Phoenix sylvestris) using homology driven proteomics. J Proteomics 2017; 165:1-10. [PMID: 28535932 DOI: 10.1016/j.jprot.2017.05.021] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 05/05/2017] [Accepted: 05/17/2017] [Indexed: 11/19/2022]
Abstract
Pollen grains from Phoenix sylvestris (date palm), a commonly cultivated tree in India has been found to cause severe allergic diseases in an increasing percentage of hypersensitive individuals. To unearth its allergenic components, pollen protein were profiled by two-dimensional gel electrophoresis followed by immunoblotting with date palm pollen sensitive patient sera. Allergens were identified by MALDI-TOF/TOF employing a layered proteomic approach combining conventional database dependent search and manual de novo sequencing followed by homology-based search as Phoenix sylvestris is unsequenced. Derivatization of tryptic peptides by acetylation has been demonstrated to differentiate the 'b' from the 'y' ions facilitating efficient de novo sequencing. Ten allergenic proteins were identified, out of which six showed homology with known allergens while others were reported for the first time. Amongst these, isoflavone reductase, beta-conglycinin, S-adenosyl methionine synthase, 1, 4 glucan synthase and beta-galactosidase were commonly reported as allergens from coconut pollen and presumably responsible for cross-reactivity. One of the allergens had IgE binding epitope recognized by its glycan moiety. The allergenic potency of date palm pollen has been demonstrated using in vitro tests. The identified allergens can be used to develop vaccines for immunotherapy against date palm pollen allergy. THE SIGNIFICANCE OF THE STUDY Identification of allergenic proteins from sources harboring them is essential in developing therapeutic interventions. This is the first comprehensive study on the identification of allergens from Phoenix sylvestris (date palm) pollen, one of the major aeroallergens in India using a proteomic approach. Proteomic methods are being increasingly used to identify allergens. However, since many of these proteins arise from species which are un-sequenced, it becomes difficult to interpret those using conventional proteomics. Date palm being an unsequenced species, the IgE-reactive proteins have been identified using a stratified proteomic workflow incorporating manual de novo sequencing and homology-based proteomics. This study also gives an insight into the presence of glycan nature of the IgE binding epitopes. Five proteins have been found to be common with coconut pollen allergens and presumably responsible for cross-reactivity. These can be used in diagnostics to differentiate patient cohorts allergic to both coconut and date palm pollen from true date palm pollen allergic subjects. This would also determine better specific immunotherapy regimes between the two cohorts. The allergens identified herein have potential towards vaccine development in date palm pollen allergy as well as in enriching the existing catalogue of allergenic proteins.
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Affiliation(s)
- Bodhisattwa Saha
- Division of Plant Biology, Bose Institute, 93/1 Acharya Prafulla Chandra Road, Kolkata 700009, India
| | - Swati Gupta Bhattacharya
- Division of Plant Biology, Bose Institute, 93/1 Acharya Prafulla Chandra Road, Kolkata 700009, India.
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Sen KI, Tang WH, Nayak S, Kil YJ, Bern M, Ozoglu B, Ueberheide B, Davis D, Becker C. Automated Antibody De Novo Sequencing and Its Utility in Biopharmaceutical Discovery. J Am Soc Mass Spectrom 2017; 28:803-810. [PMID: 28105549 PMCID: PMC5392168 DOI: 10.1007/s13361-016-1580-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 12/02/2016] [Accepted: 12/04/2016] [Indexed: 05/12/2023]
Abstract
Applications of antibody de novo sequencing in the biopharmaceutical industry range from the discovery of new antibody drug candidates to identifying reagents for research and determining the primary structure of innovator products for biosimilar development. When murine, phage display, or patient-derived monoclonal antibodies against a target of interest are available, but the cDNA or the original cell line is not, de novo protein sequencing is required to humanize and recombinantly express these antibodies, followed by in vitro and in vivo testing for functional validation. Availability of fully automated software tools for monoclonal antibody de novo sequencing enables efficient and routine analysis. Here, we present a novel method to automatically de novo sequence antibodies using mass spectrometry and the Supernovo software. The robustness of the algorithm is demonstrated through a series of stress tests. Graphical Abstract ᅟ.
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Affiliation(s)
- K Ilker Sen
- Protein Metrics Inc, 1622 San Carlos Ave, Suite C, San Carlos, CA, 94070, USA.
| | - Wilfred H Tang
- Protein Metrics Inc, 1622 San Carlos Ave, Suite C, San Carlos, CA, 94070, USA
| | - Shruti Nayak
- Langone Medical Center, New York University, 430 East 29th street, 8th floor room 860, New York, NY, 10016, USA
| | - Yong J Kil
- Protein Metrics Inc, 1622 San Carlos Ave, Suite C, San Carlos, CA, 94070, USA
| | - Marshall Bern
- Protein Metrics Inc, 1622 San Carlos Ave, Suite C, San Carlos, CA, 94070, USA
| | - Berk Ozoglu
- Janssen Research and Development, LLC, 1400 McKean Road, Spring House, PA, 19477, USA
| | - Beatrix Ueberheide
- Langone Medical Center, New York University, 430 East 29th street, 8th floor room 860, New York, NY, 10016, USA
| | - Darryl Davis
- Janssen Research and Development, LLC, 1400 McKean Road, Spring House, PA, 19477, USA
| | - Christopher Becker
- Protein Metrics Inc, 1622 San Carlos Ave, Suite C, San Carlos, CA, 94070, USA
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Abstract
Through advances in molecular biology, comparative analysis of DNA sequences is currently the cornerstone in the study of molecular evolution and phylogenetics. Nevertheless, protein mass spectrometry offers some unique opportunities to enable phylogenetic analyses in organisms where DNA may be difficult or costly to obtain. To date, the methods of phylogenetic analysis using protein mass spectrometry can be classified into three categories: (1) de novo protein sequencing followed by classical phylogenetic reconstruction, (2) direct phylogenetic reconstruction using proteolytic peptide mass maps, and (3) mapping of mass spectral data onto classical phylogenetic trees. In this chapter, we provide a brief description of the three methods and the protocol for each method along with relevant tools and algorithms.
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Affiliation(s)
- Shiyong Ma
- Prince of Wales Clinical School, UNSW Australia, Sydney, NSW, 2052, Australia
- Lowy Cancer Research Centre, UNSW, Corner of High and Botany St, Kensington, NSW, 2033, Australia
| | - Kevin M Downard
- Prince of Wales Clinical School, UNSW Australia, Sydney, NSW, 2052, Australia
- Lowy Cancer Research Centre, UNSW, Corner of High and Botany St, Kensington, NSW, 2033, Australia
| | - Jason W H Wong
- Prince of Wales Clinical School, UNSW Australia, Sydney, NSW, 2052, Australia.
- Lowy Cancer Research Centre, UNSW, Corner of High and Botany St, Kensington, NSW, 2033, Australia.
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35
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Novák J, Sokolová L, Lemr K, Pluháček T, Palyzová A, Havlíček V. Batch-processing of imaging or liquid-chromatography mass spectrometry datasets and De Novo sequencing of polyketide siderophores. Biochim Biophys Acta Proteins Proteom 2016; 1865:768-775. [PMID: 27956353 DOI: 10.1016/j.bbapap.2016.12.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 12/02/2016] [Accepted: 12/08/2016] [Indexed: 11/18/2022]
Abstract
The open-source and cross-platform software CycloBranch was utilized for dereplication of organic compounds from mass spectrometry imaging imzML datasets and its functions were illustrated on microbial siderophores. The pixel-to-pixel batch-processing was analogous to liquid chromatography mass spectrometry data. Each data point represented here by accurate m/z values and the corresponding ion intensities was matched against integrated compound libraries. The fine isotopic structure matching was also embedded into CycloBranch dereplication process. The siderophores' characterization from single-pixel mass spectra was further supported by their de novo sequencing. New ketide building block library was utilized by CycloBranch to characterize the siderophores in images and mixtures and nomenclature of fragment ion series of linear and cyclic polyketide siderophores was proposed. The software is freely available at http://ms.biomed.cas.cz/cyclobranch. This article is part of a Special Issue entitled: MALDI Imaging, edited by Dr. Corinna Henkel and Prof. Peter Hoffmann.
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Affiliation(s)
- Jiří Novák
- Institute of Microbiology of the ASCR, v.v.i., Videnska 1083, 142 20 Prague 4, Czech Republic.
| | - Lucie Sokolová
- Institute of Microbiology of the ASCR, v.v.i., Videnska 1083, 142 20 Prague 4, Czech Republic
| | - Karel Lemr
- Institute of Microbiology of the ASCR, v.v.i., Videnska 1083, 142 20 Prague 4, Czech Republic
| | - Tomáš Pluháček
- Institute of Microbiology of the ASCR, v.v.i., Videnska 1083, 142 20 Prague 4, Czech Republic
| | - Andrea Palyzová
- Institute of Microbiology of the ASCR, v.v.i., Videnska 1083, 142 20 Prague 4, Czech Republic
| | - Vladimír Havlíček
- Institute of Microbiology of the ASCR, v.v.i., Videnska 1083, 142 20 Prague 4, Czech Republic.
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Fan CY, Huang SY, Chou MY, Lyu PC. De novo protein sequencing, humanization and in vitro effects of an antihuman CD34 mouse monoclonal antibody. Biochem Biophys Rep 2016; 9:51-60. [PMID: 28955989 PMCID: PMC5614552 DOI: 10.1016/j.bbrep.2016.11.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2016] [Revised: 10/25/2016] [Accepted: 11/15/2016] [Indexed: 01/08/2023] Open
Abstract
QBEND/10 is a mouse immunoglobulin lambda-chain monoclonal antibody with strict specificity against human hematopoietic progenitor cell antigen CD34. Our in vitro study showed that QBEND/10 impairs the tube formation of human umbilical vein endothelial cells (HUVECs), suggesting that the antibody may be of potential benefit in blocking tumor angiogenesis. We provided a de novo protein sequencing method through tandem mass spectrometry to identify the amino acid sequences in the variable heavy and light chains of QBEND/10. To reduce immunogenicity for clinical applications, QBEND/10 was further humanized using the resurfacing approach. We demonstrate that the de novo sequenced and humanized QBEND/10 retains the biological functions of the parental mouse counterpart, including the binding kinetics to CD34 and blockage of the tube formation of the HUVECs.
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Affiliation(s)
- Chia-Yu Fan
- Institute of Bioinformatics and Structural Biology & Department of Life Science, National Tsing Hua University, Hsinchu, Taiwan.,Biomedical Technology and Device Research Laboratories, Industrial Technology Research Institute, Hsinchu, Taiwan
| | | | - Min-Yuan Chou
- Biomedical Technology and Device Research Laboratories, Industrial Technology Research Institute, Hsinchu, Taiwan
| | - Ping-Chiang Lyu
- Institute of Bioinformatics and Structural Biology & Department of Life Science, National Tsing Hua University, Hsinchu, Taiwan
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Zhang GH, Jiang NH, Song WL, Ma CH, Yang SC, Chen JW. De novo Sequencing and Transcriptome Analysis of Pinellia ternata Identify the Candidate Genes Involved in the Biosynthesis of Benzoic Acid and Ephedrine. Front Plant Sci 2016; 7:1209. [PMID: 27579029 PMCID: PMC4986801 DOI: 10.3389/fpls.2016.01209] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Accepted: 07/29/2016] [Indexed: 06/06/2023]
Abstract
BACKGROUND The medicinal herb, Pinellia ternata, is purported to be an anti-emetic with analgesic and sedative effects. Alkaloids are the main biologically active compounds in P. ternata, especially ephedrine that is a phenylpropylamino alkaloid specifically produced by Ephedra and Catha edulis. However, how ephedrine is synthesized in plants is uncertain. Only the phenylalanine ammonia lyase (PAL) and relevant genes in this pathway have been characterized. Genomic information of P. ternata is also unavailable. RESULTS We analyzed the transcriptome of the tuber of P. ternata with the Illumina HiSeq™ 2000 sequencing platform. 66,813,052 high-quality reads were generated, and these reads were assembled de novo into 89,068 unigenes. Most known genes involved in benzoic acid biosynthesis were identified in the unigene dataset of P. ternata, and the expression patterns of some ephedrine biosynthesis-related genes were analyzed by reverse transcription quantitative real-time PCR (RT-qPCR). Also, 14,468 simple sequence repeats (SSRs) were identified from 12,000 unigenes. Twenty primer pairs for SSRs were randomly selected for the validation of their amplification effect. CONCLUSION RNA-seq data was used for the first time to provide a comprehensive gene information on P. ternata at the transcriptional level. These data will advance molecular genetics in this valuable medicinal plant.
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Gorshkov V, Hotta SYK, Verano-Braga T, Kjeldsen F. Peptide de novo sequencing of mixture tandem mass spectra. Proteomics 2016; 16:2470-9. [PMID: 27329701 PMCID: PMC5297990 DOI: 10.1002/pmic.201500549] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2015] [Revised: 04/27/2016] [Accepted: 06/17/2016] [Indexed: 02/02/2023]
Abstract
The impact of mixture spectra deconvolution on the performance of four popular de novo sequencing programs was tested using artificially constructed mixture spectra as well as experimental proteomics data. Mixture fragmentation spectra are recognized as a limitation in proteomics because they decrease the identification performance using database search engines. De novo sequencing approaches are expected to be even more sensitive to the reduction in mass spectrum quality resulting from peptide precursor co‐isolation and thus prone to false identifications. The deconvolution approach matched complementary b‐, y‐ions to each precursor peptide mass, which allowed the creation of virtual spectra containing sequence specific fragment ions of each co‐isolated peptide. Deconvolution processing resulted in equally efficient identification rates but increased the absolute number of correctly sequenced peptides. The improvement was in the range of 20–35% additional peptide identifications for a HeLa lysate sample. Some correct sequences were identified only using unprocessed spectra; however, the number of these was lower than those where improvement was obtained by mass spectral deconvolution. Tight candidate peptide score distribution and high sensitivity to small changes in the mass spectrum introduced by the employed deconvolution method could explain some of the missing peptide identifications.
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Affiliation(s)
- Vladimir Gorshkov
- Department of Biochemistry and Molecular Biology, University of Southern Denmark Odense M, Odense, Denmark.
| | | | - Thiago Verano-Braga
- Department of Biochemistry and Molecular Biology, University of Southern Denmark Odense M, Odense, Denmark.,Department of Physiology and Biophysics, Federal University of Minas Gerais Belo Horizonte - MG, Belo Horizonte, Brazil
| | - Frank Kjeldsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark Odense M, Odense, Denmark
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Muth T, Kolmeder CA, Salojärvi J, Keskitalo S, Varjosalo M, Verdam FJ, Rensen SS, Reichl U, de Vos WM, Rapp E, Martens L. Navigating through metaproteomics data: a logbook of database searching. Proteomics 2015; 15:3439-53. [PMID: 25778831 DOI: 10.1002/pmic.201400560] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Revised: 02/13/2015] [Accepted: 03/06/2015] [Indexed: 11/12/2022]
Abstract
Metaproteomic research involves various computational challenges during the identification of fragmentation spectra acquired from the proteome of a complex microbiome. These issues are manifold and range from the construction of customized sequence databases, the optimal setting of search parameters to limitations in the identification search algorithms themselves. In order to assess the importance of these individual factors, we studied the effect of strategies to combine different search algorithms, explored the influence of chosen database search settings, and investigated the impact of the size of the protein sequence database used for identification. Furthermore, we applied de novo sequencing as a complementary approach to classic database searching. All evaluations were performed on a human intestinal metaproteome dataset. Pyrococcus furiosus proteome data were used to contrast database searching of metaproteomic data to a classic proteomic experiment. Searching against subsets of metaproteome databases and the use of multiple search engines increased the number of identifications. The integration of P. furiosus sequences in a metaproteomic sequence database showcased the limitation of the target-decoy-controlled false discovery rate approach in combination with large sequence databases. The selection of varying search engine parameters and the application of de novo sequencing represented useful methods to increase the reliability of the results. Based on our findings, we provide recommendations for the data analysis that help researchers to establish or improve analysis workflows in metaproteomics.
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Affiliation(s)
- Thilo Muth
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Carolin A Kolmeder
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Jarkko Salojärvi
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Salla Keskitalo
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Markku Varjosalo
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Froukje J Verdam
- Department of General Surgery, NUTRIM, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Sander S Rensen
- Department of General Surgery, NUTRIM, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Udo Reichl
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany.,Otto-von-Guericke University, Bioprocess Engineering, Magdeburg, Germany
| | - Willem M de Vos
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland.,Department of Bacteriology and Immunology, University of Helsinki, Helsinki, Finland.,Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Erdmann Rapp
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Lennart Martens
- Department of Biochemistry, Ghent University, Ghent, Belgium.,Department of Medical Protein Research, VIB, Ghent, Belgium
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40
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Abstract
The aim of this chapter is to give a short introduction to peptide analysis by mass spectrometry (MS) and interpretation of fragment mass spectra. Through examples and guidelines we demonstrate how to understand and validate search results and how to perform de novo sequencing based on the often very complex fragmentation pattern obtained by tandem mass spectrometry (also referred to as MSMS). The focus is on simple rules for interpretation of MSMS spectra of tryptic as well as non-tryptic peptides.
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Affiliation(s)
- Karin Hjernø
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Peter Højrup
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark.
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41
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González-Morales L, Pedraza-Escalona M, Diego-Garcia E, Restano-Cassulini R, Batista CVF, Gutiérrez MDC, Possani LD. Proteomic characterization of the venom and transcriptomic analysis of the venomous gland from the Mexican centipede Scolopendra viridis. J Proteomics 2014; 111:224-37. [PMID: 24780725 DOI: 10.1016/j.jprot.2014.04.033] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 04/16/2014] [Accepted: 04/18/2014] [Indexed: 11/29/2022]
Abstract
UNLABELLED This communication reports the results of proteomic, transcriptomic, biochemical and electrophysiological analysis of the soluble venom and venom glands of the Mexican centipede Scolopendra viridis Say (here thereafter abbreviated S. viridis). Separation of the soluble venom permitted to obtain 54 different fractions, from which a mass finger printing analysis permitted the identification of at least 86 components, where 70% of the molecules have low molecular masses. Two-dimensional electrophoretic separation of this venom revealed the presence of about forty proteins with molecular weights ranging from 17 to 58kDa. The novo sequencing of 149 peptides obtained by LC-MS/MS from the 2D-gels showed the presence of proteins with amino acid sequences similar to several enzymes and venom allergens type 3. Furthermore, a total of 180 sequences were obtained from a cDNA library prepared with two venomous glands. From this, 155 sequences correspond to complete genes containing more than 200 base pairs each. Comparative sequence analyses of these sequences indicated the presence of different types of enzymes and toxin-like genes. Two proteins with molecular weights around 37,000 and 42,000Da were shown to contain hyaluronidase activity. Electrophysiological assays performed with soluble venom show that it decreases mammalian sodium channel currents. BIOLOGICAL SIGNIFICANCE Animal venoms of Scolopendra species have been scarcely studied, although they have been reported to contain several bioactive compounds, some of which with potential therapeutic interest. The Mexican centipede S. viridis contains a powerful venom, capable of inflicting immediate effects on their preys. This communication is focused on the identification and description of a proteomic and transcriptomic analysis of the protein components of this venom. Several amino acid sequences similar to reported enzymes are the principal components in the S. viridis venom, but also a low number of toxins were identified. This knowledge should contribute to the understanding of the pharmacological effects caused by bites of this centipede species.
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Affiliation(s)
- Lidia González-Morales
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad, 2001, Cuernavaca 62210, Mexico; Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca 62209, Mexico
| | - Martha Pedraza-Escalona
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad, 2001, Cuernavaca 62210, Mexico
| | - Elia Diego-Garcia
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad, 2001, Cuernavaca 62210, Mexico
| | - Rita Restano-Cassulini
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad, 2001, Cuernavaca 62210, Mexico
| | - Cesar V F Batista
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad, 2001, Cuernavaca 62210, Mexico
| | - Maria del Carmen Gutiérrez
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca 62209, Mexico
| | - Lourival D Possani
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad, 2001, Cuernavaca 62210, Mexico.
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Merlot S, Hannibal L, Martins S, Martinelli L, Amir H, Lebrun M, Thomine S. The metal transporter PgIREG1 from the hyperaccumulator Psychotria gabriellae is a candidate gene for nickel tolerance and accumulation. J Exp Bot 2014; 65:1551-64. [PMID: 24510940 DOI: 10.1093/jxb/eru025] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Nickel is an economically important metal and phytotechnologies are being developed to limit the impact of nickel mining on the environment. More than 300 plant species are known to hyperaccumulate nickel. However, our knowledge of the mechanisms involved in nickel accumulation in plants is very limited because it has not yet been possible to study these hyperaccumulators at the genomic level. Here, we used next-generation sequencing technologies to sequence the transcriptome of the nickel hyperaccumulator Psychotria gabriellae of the Rubiaceae family, and used yeast and Arabidopsis as heterologous systems to study the activity of identified metal transporters. We characterized the activity of three metal transporters from the NRAMP and IREG/FPN families. In particular, we showed that PgIREG1 is able to confer nickel tolerance when expressed in yeast and in transgenic plants, where it localizes in the tonoplast. In addition, PgIREG1 shows higher expression in P. gabriellae than in the related non-accumulator species Psychotria semperflorens. Our results designate PgIREG1 as a candidate gene for nickel tolerance and hyperaccumulation in P. gabriellae. These results also show how next-generation sequencing technologies can be used to access the transcriptome of non-model nickel hyperaccumulators to identify the underlying molecular mechanisms.
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Affiliation(s)
- Sylvain Merlot
- CNRS, Institut des Sciences du Végétal, Labex SPS, Avenue de la terrasse, 91198 Gif-sur-Yvette cedex, France
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Jia C, Lietz CB, Ye H, Hui L, Yu Q, Yoo S, Li L. A multi-scale strategy for discovery of novel endogenous neuropeptides in the crustacean nervous system. J Proteomics 2013; 91:1-12. [PMID: 23806756 DOI: 10.1016/j.jprot.2013.06.021] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Revised: 05/26/2013] [Accepted: 06/16/2013] [Indexed: 12/18/2022]
Abstract
UNLABELLED The conventional mass spectrometry (MS)-based strategy is often inadequate for the comprehensive characterization of various size neuropeptides without the assistance of genomic information. This study evaluated sequence coverage of different size neuropeptides in two crustacean species, blue crab Callinectes sapidus and Jonah crab Cancer borealis using conventional MS methodologies and revealed limitations to mid- and large-size peptide analysis. Herein we attempt to establish a multi-scale strategy for simultaneous and confident sequence elucidation of various sizes of peptides in the crustacean nervous system. Nine novel neuropeptides spanning a wide range of molecular weights (0.9-8.2kDa) were fully sequenced from a major neuroendocrine organ, the sinus gland of the spiny lobster Panulirus interruptus. These novel neuropeptides included seven allatostatin (A- and B-type) peptides, one crustacean hyperglycemic hormone precursor-related peptide, and one crustacean hyperglycemic hormone. Highly accurate multi-scale characterization of a collection of varied size neuropeptides was achieved by integrating traditional data-dependent tandem MS, improved bottom-up sequencing, multiple fragmentation technique-enabled top-down sequencing, chemical derivatization, and in silico homology search. Collectively, the ability to characterize a neuropeptidome with vastly differing molecule sizes from a neural tissue extract could find great utility in unraveling complex signaling peptide mixtures employed by other biological systems. BIOLOGICAL SIGNIFICANCE Mass spectrometry (MS)-based neuropeptidomics aims to completely characterize the neuropeptides in a target organism as an important first step toward a better understanding of the structure and function of these complex signaling molecules. Although liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) with data-dependent acquisition is a powerful tool in peptidomic research, it often lacks the capability for de novo sequencing of mid-size and large peptides due to inefficient fragmentation of peptides larger than 4kDa. This study describes a multi-scale strategy for complete and confident sequence elucidation of various sizes of neuropeptides in the crustacean nervous system. The aim is to fill a technical gap where the conventional strategy is inefficient for comprehensive characterization of a complex neuropeptidome without assistance of genomic information. Nine novel neuropeptides in a wide range of molecular weights (0.9-8.2kDa) were fully sequenced from a major neuroendocrine organ of the spiny lobster, P. interruptus. The resulting molecular information extracted from such multi-scale peptidomic analysis will greatly accelerate functional studies of these novel neuropeptides.
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Affiliation(s)
- Chenxi Jia
- School of Pharmacy, University of Wisconsin-Madison, WI, USA; Department of Chemistry, University of Wisconsin-Madison, WI, USA
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44
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Rogowska-Wrzesinska A, Le Bihan MC, Thaysen-Andersen M, Roepstorff P. 2D gels still have a niche in proteomics. J Proteomics. 2013;88:4-13. [PMID: 23353020 DOI: 10.1016/j.jprot.2013.01.010] [Citation(s) in RCA: 141] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Revised: 01/09/2013] [Accepted: 01/11/2013] [Indexed: 01/26/2023]
Abstract
With the rapid advance of MS-based proteomics one might think that 2D gel-based proteomics is dead. This is far from the truth. Current research has shown that there are still a number of places in the field of protein and molecular biology where 2D gels still play a leading role. The aim of this review is to highlight some of these applications. Examples from our own research as well as from other published works are used to illustrate the 2D gel driven research in the areas of: 1) de novo sequencing and protein identification from organisms with no or incomplete genome sequences available; 2) alternative detection methods for modification specific proteomics; 3) identification of protein isoforms and modified proteins. With an example of the glycoprotein TIMP-1 protein we illustrate the unique properties of 2D gels for the separation and characterisation of multiply modified proteins. We also show that careful analysis of experimental and theoretical protein mass and pI can lead to the identification of unanticipated protein variants modified by for example proteolytic cleavage. Together this shows that there is an important niche for 2D gel-based proteomics, which compliments traditional LC-MS techniques for specific protein research purposes.
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