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Santos Junior MN, Santos RS, Neves WS, Fernandes JM, de Brito Guimarães BC, Barbosa MS, Silva LSC, Gomes CP, Rezende IS, Oliveira CNT, de Macêdo Neres NS, Campos GB, Bastos BL, Timenetsky J, Marques LM. Immunoinformatics and analysis of antigen distribution of Ureaplasma diversum strains isolated from different Brazilian states. BMC Vet Res 2020; 16:379. [PMID: 33028315 PMCID: PMC7542862 DOI: 10.1186/s12917-020-02602-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 09/30/2020] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND Ureaplasma diversum has numerous virulence factors that contribute to pathogenesis in cattle, including Lipid-associated membrane proteins (LAMPs). Therefore, the objectives of this study were to evaluate in silico important characteristics for immunobiological applications and for heterologous expression of 36 LAMPs of U. diversum (UdLAMPs) and, also, to verify by conventional PCR the distribution of these antigens in strains of Brazilian states (Bahia, Minas Gerais, São Paulo, and Mato Grosso do Sul). The Manatee database was used to obtain the gene and peptide sequences of the antigens. Similarity and identity studies were performed using BLASTp and direct antigenicity was evaluated by the VaxiJen v2.0 server. Epitope prediction for B lymphocytes was performed on the BepiPred v2.0 and CBTOPE v1.0 servers. NetBoLApan v1.0 was used to predict CD8+ T lymphocyte epitopes. Subcellular location and presence of transmembrane regions were verified by the software PSORTb v3.0.2 and TMHMM v2.2 respectively. SignalP v5.0, SecretomeP v2.0, and DOLOP servers were used to predict the extracellular excretion signal. Physico-chemical properties were evaluated by the web-software ProtParam, Solpro, and Protein-sol. RESULTS In silico analysis revealed that many UdLAMPs have desirable properties for immunobiological applications and heterologous expression. The proteins gudiv_61, gudiv_103, gudiv_517, and gudiv_681 were most promising. Strains from the 4 states were PCR positive for antigens predicted with immunogenic and/or with good characteristics for expression in a heterologous system. CONCLUSION These works contribute to a better understanding of the immunobiological properties of the UdLAMPs and provide a profile of the distribution of these antigens in different Brazilian states.
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Affiliation(s)
- Manoel Neres Santos Junior
- Department of Biointeraction, Multidisciplinary Institute of Health, Universidade Federal da Bahia, Rua Hormindo Barros, 58 - Quadra 17 - Lote 58, Bairro Candeias - CEP: 45.029-094, Vitória da Conquista, BA, Brazil.,Department of Microbiology, State University of Santa Cruz (UESC), Ilhéus, Brazil
| | - Ronaldo Silva Santos
- Department of Biointeraction, Multidisciplinary Institute of Health, Universidade Federal da Bahia, Rua Hormindo Barros, 58 - Quadra 17 - Lote 58, Bairro Candeias - CEP: 45.029-094, Vitória da Conquista, BA, Brazil
| | - Wanderson Souza Neves
- Department of Biointeraction, Multidisciplinary Institute of Health, Universidade Federal da Bahia, Rua Hormindo Barros, 58 - Quadra 17 - Lote 58, Bairro Candeias - CEP: 45.029-094, Vitória da Conquista, BA, Brazil
| | - Janaina Marinho Fernandes
- Department of Biointeraction, Multidisciplinary Institute of Health, Universidade Federal da Bahia, Rua Hormindo Barros, 58 - Quadra 17 - Lote 58, Bairro Candeias - CEP: 45.029-094, Vitória da Conquista, BA, Brazil
| | | | - Maysa Santos Barbosa
- Department of Microbiology, Institute of Biomedical Science, University of São Paulo, São Paulo, Brazil
| | | | - Camila Pacheco Gomes
- Department of Microbiology, State University of Santa Cruz (UESC), Ilhéus, Brazil
| | - Izadora Souza Rezende
- Department of Microbiology, Institute of Biomedical Science, University of São Paulo, São Paulo, Brazil
| | - Caline Novaes Teixeira Oliveira
- Department of Biointeraction, Multidisciplinary Institute of Health, Universidade Federal da Bahia, Rua Hormindo Barros, 58 - Quadra 17 - Lote 58, Bairro Candeias - CEP: 45.029-094, Vitória da Conquista, BA, Brazil.,Department of Microbiology, State University of Santa Cruz (UESC), Ilhéus, Brazil
| | - Nayara Silva de Macêdo Neres
- Department of Biointeraction, Multidisciplinary Institute of Health, Universidade Federal da Bahia, Rua Hormindo Barros, 58 - Quadra 17 - Lote 58, Bairro Candeias - CEP: 45.029-094, Vitória da Conquista, BA, Brazil
| | - Guilherme Barreto Campos
- Department of Biointeraction, Multidisciplinary Institute of Health, Universidade Federal da Bahia, Rua Hormindo Barros, 58 - Quadra 17 - Lote 58, Bairro Candeias - CEP: 45.029-094, Vitória da Conquista, BA, Brazil
| | - Bruno Lopes Bastos
- Department of Biointeraction, Multidisciplinary Institute of Health, Universidade Federal da Bahia, Rua Hormindo Barros, 58 - Quadra 17 - Lote 58, Bairro Candeias - CEP: 45.029-094, Vitória da Conquista, BA, Brazil
| | - Jorge Timenetsky
- Department of Microbiology, Institute of Biomedical Science, University of São Paulo, São Paulo, Brazil
| | - Lucas Miranda Marques
- Department of Biointeraction, Multidisciplinary Institute of Health, Universidade Federal da Bahia, Rua Hormindo Barros, 58 - Quadra 17 - Lote 58, Bairro Candeias - CEP: 45.029-094, Vitória da Conquista, BA, Brazil. .,Department of Microbiology, State University of Santa Cruz (UESC), Ilhéus, Brazil. .,Department of Microbiology, Institute of Biomedical Science, University of São Paulo, São Paulo, Brazil.
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Liang Y, Jin Y, Wu Z, Tucholski T, Brown KA, Zhang L, Zhang Y, Ge Y. Bridged Hybrid Monolithic Column Coupled to High-Resolution Mass Spectrometry for Top-Down Proteomics. Anal Chem 2019; 91:1743-1747. [PMID: 30668094 DOI: 10.1021/acs.analchem.8b05817] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Top-down mass spectrometry (MS)-based proteomics has become a powerful tool for comprehensive characterization of intact proteins. However, because of the high complexity of the proteome, highly effective separation of intact proteins from complex mixtures prior to MS analysis remains challenging. Monolithic columns have shown great promise for intact protein separation due to their high permeability, low backpressure, and fast mass transfer. Herein, for the first time, we developed bridged hybrid bis(triethoxysilyl)ethylene (BTSEY) monolith with C8 functional groups (C8@BTSEY) for highly effective protein separation and coupled it to high-resolution MS for identification of intact proteins from complex protein mixtures. We have optimized mobile phase conditions of our monolith-based reverse-phase chromatography (RPC) for online liquid chromatography (LC)-MS analysis and evaluated separation reproducibility of the C8@BTSEY column. We further assessed the chromatographic performance of this column by separating a complex protein mixture extracted from swine heart tissue. Using our monolithic column (i.d. 100 μm × 35 cm), we separated over 300 proteoforms (up to 104 kDa) from 360 ng of protein mixture in an 80 min one-dimensional (1D) LC run. The highly effective separation and recovery of intact proteins from this monolithic column allowed unambiguous identification of ∼100 proteoforms including a large protein, αactinin2 (103.77 kDa), by online 1D LC-MS/MS analysis for the first time. As demonstrated, this C8@BTSEY column is reproducible and effective in separation of intact proteins, which shows high promise for top-down proteomics.
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Affiliation(s)
- Yu Liang
- Department of Cell and Regenerative Biology , University of Wisconsin-Madison , Madison , Wisconsin 53705 , United States.,CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center , Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian , Liaoning 116023 , China
| | - Yutong Jin
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - Zhijie Wu
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - Trisha Tucholski
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - Kyle A Brown
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - Lihua Zhang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center , Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian , Liaoning 116023 , China
| | - Yukui Zhang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center , Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian , Liaoning 116023 , China
| | - Ying Ge
- Department of Cell and Regenerative Biology , University of Wisconsin-Madison , Madison , Wisconsin 53705 , United States.,Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States.,Human Proteomics Program, School of Medicine and Public Health , University of Wisconsin-Madison , Madison , Wisconsin 53705 , United States
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Zhang C, Allegretti M, Vonck J, Langer JD, Marcia M, Peng G, Michel H. Production of fully assembled and active Aquifex aeolicus F1FO ATP synthase in Escherichia coli. Biochim Biophys Acta Gen Subj 2013; 1840:34-40. [PMID: 24005236 DOI: 10.1016/j.bbagen.2013.08.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Revised: 08/13/2013] [Accepted: 08/27/2013] [Indexed: 11/29/2022]
Abstract
BACKGROUND F1FO ATP synthases catalyze the synthesis of ATP from ADP and inorganic phosphate driven by ion motive forces across the membrane. A number of ATP synthases have been characterized to date. The one from the hyperthermophilic bacterium Aquifex aeolicus presents unique features, i.e. a putative heterodimeric stalk. To complement previous work on the native form of this enzyme, we produced it heterologously in Escherichia coli. METHODS We designed an artificial operon combining the nine genes of A. aeolicus ATP synthase, which are split into four clusters in the A. aeolicus genome. We expressed the genes and purified the enzyme complex by affinity and size-exclusion chromatography. We characterized the complex by native gel electrophoresis, Western blot, and mass spectrometry. We studied its activity by enzymatic assays and we visualized its structure by single-particle electron microscopy. RESULTS We show that the heterologously produced complex has the same enzymatic activity and the same structure as the native ATP synthase complex extracted from A. aeolicus cells. We used our expression system to confirm that A. aeolicus ATP synthase possesses a heterodimeric peripheral stalk unique among non-photosynthetic bacterial F1FO ATP synthases. CONCLUSIONS Our system now allows performing previously impossible structural and functional studies on A. aeolicus F1FO ATP synthase. GENERAL SIGNIFICANCE More broadly, our work provides a valuable platform to characterize many other membrane protein complexes with complicated stoichiometry, i.e. other respiratory complexes, the nuclear pore complex, or transporter systems.
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Affiliation(s)
- Chunli Zhang
- Max Planck Institute of Biophysics, Department of Molecular Membrane Biology, Max-von-Laue-Str. 3, D-60438 Frankfurt am Main, Germany
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