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Luciani M, Krasteva I, Di Febo T, Perletta F, D'Onofrio F, De Massis F, D'Alterio N, Sacchini F, Tittarelli M. Proteomics and bioinformatics investigations to improve serological diagnosis of canine brucellosis. Proteomics Clin Appl 2023; 17:e2200116. [PMID: 37532634 DOI: 10.1002/prca.202200116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 07/10/2023] [Accepted: 07/25/2023] [Indexed: 08/04/2023]
Abstract
PURPOSE Brucella canis is pathogenic for dogs and humans. Serological diagnosis is a cost-effective approach for disease surveillance, but a major drawback of current serological tests is the cross-reactivity with other bacteria that results in false positive reactions. Development of indirect tests with improved sensitivity and specificity that use selected B. canis proteins instead of the whole antigen remain a priority. EXPERIMENTAL DESIGN A western blotting assay was developed to define the serum antibody patterns associated to infection using a panel of positive and negative dog sera. B. canis positive sera recognized immunogenic bands ranging from 7 to 30 kDa that were then submitted to ESI-LC-MS/MS and analyzed by bioinformatics tools. RESULTS A total of 398 B. canis proteins were identified. Bioinformatics tools identified 16 non cytoplasmic immunogenic proteins predicted as non-homologous with the most important Brucella cross-reactive bacteria and nine B. canis proteins non-homologous to B. ovis; among the latter, one resulted non-homologous to B. melitensis. Data are available via ProteomeXchange with identifier PXD042682. CONCLUSIONS AND CLINICAL RELEVANCE The western blotting test developed was able to distinguish between infected and non-infected animals and may serve as a confirmatory test for the serological diagnosis of B. canis. The mass spectrometry and in silico results lead to the identification of specific candidate antigens that pave the way for the development of more accurate indirect diagnostic tests.
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Affiliation(s)
- Mirella Luciani
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, Teramo, Italy
| | - Ivanka Krasteva
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, Teramo, Italy
| | - Tiziana Di Febo
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, Teramo, Italy
| | - Fabrizia Perletta
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, Teramo, Italy
| | - Federica D'Onofrio
- Faculty of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Teramo, Italy
| | - Fabrizio De Massis
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, Teramo, Italy
| | - Nicola D'Alterio
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, Teramo, Italy
| | - Flavio Sacchini
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, Teramo, Italy
| | - Manuela Tittarelli
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, Teramo, Italy
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Husain AA, Pinto SM, Subbannayya Y, Kapoor S, Khulkhule P, Bhartiya N, Prasad TSK, Daginawala HF, Singh LR, Kashyap RS. Development of multiple reaction monitoring (MRM) assays to identify Brucella abortus proteins in the serum of humans and livestock. Proteomics Clin Appl 2023; 17:e2200009. [PMID: 35925648 DOI: 10.1002/prca.202200009] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 06/30/2022] [Accepted: 08/03/2022] [Indexed: 01/25/2023]
Abstract
In the present study, a targeted multiple reaction monitoring-mass spectrometry (MRM-MS) approach was developed to screen and identify protein biomarkers for brucellosis in humans and livestock. The selection of proteotypic peptides was carried out by generating in silico tryptic peptides of the Brucella proteome. Using bioinformatics analysis, 30 synthetic peptides corresponding to 10 immunodominant Brucella abortus proteins were generated. MRM-MS assays for the accurate detection of these peptides were optimized using 117 serum samples of human and livestock stratified as clinically confirmed (45), suspected (62), and control (10). Using high throughput MRM assays, transitions for four peptides were identified in several clinically confirmed and suspected human and livestock serum samples. Of these, peptide NAIYDVVTR corresponding to B. abortus proteins: BruAb2_0537 was consistently detected in the clinically confirmed serum samples of both humans and livestock with 100% specificity. To conclude, a high throughput MRM-MS-based protocol for detecting endogenous B. abortus peptides in serum samples of humans and livestock was developed. The developed protocol will help design sensitive assays to accurately diagnose brucellosis in humans and livestock. The data associated with this study are deposited in Panorama Public (https://panoramaweb.org/rNOZCy.url with ProteomeXchange ID: PXD034407).
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Affiliation(s)
- Aliabbas A Husain
- Research Centre, Dr. G.M Taori Central India Institute of Medical Science, Nagpur, Maharashtra, India
| | - Sneha M Pinto
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Center, Yenepoya (Deemed to be University), Mangalore, India
| | - Yashwanth Subbannayya
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Center, Yenepoya (Deemed to be University), Mangalore, India
| | - Saketh Kapoor
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Center, Yenepoya (Deemed to be University), Mangalore, India
| | - Payal Khulkhule
- Research Centre, Dr. G.M Taori Central India Institute of Medical Science, Nagpur, Maharashtra, India
| | - Nidhi Bhartiya
- Research Centre, Dr. G.M Taori Central India Institute of Medical Science, Nagpur, Maharashtra, India
| | - T S Keshava Prasad
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Center, Yenepoya (Deemed to be University), Mangalore, India
| | - Hatim F Daginawala
- Research Centre, Dr. G.M Taori Central India Institute of Medical Science, Nagpur, Maharashtra, India
| | - Lokendra R Singh
- Research Centre, Dr. G.M Taori Central India Institute of Medical Science, Nagpur, Maharashtra, India
| | - Rajpal Singh Kashyap
- Research Centre, Dr. G.M Taori Central India Institute of Medical Science, Nagpur, Maharashtra, India
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3
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Wang C, Zhang C, Fu Q, Zhang N, Ding M, Zhou Z, Chen X, Zhang F, Zhang C, Zhang CY, Wang JJ. Increased serum piwi-interacting RNAs as a novel potential diagnostic tool for brucellosis. Front Cell Infect Microbiol 2022; 12:992775. [PMID: 36189348 PMCID: PMC9519857 DOI: 10.3389/fcimb.2022.992775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 08/29/2022] [Indexed: 11/24/2022] Open
Abstract
Background Piwi-interacting RNAs (piRNAs) have emerged as potential novel indicators for various diseases; however, their diagnostic value for brucellosis remains unclear. This study aimed to evaluate the diagnostic potential of altered serum piRNAs in patients with brucellosis. Methods Illumina sequencing via synthesis (SBS) technology was used to screen the serum piRNA profile in brucellosis patients, and markedly dysregulated piRNAs were confirmed by quantitative real-time polymerase chain reaction (qRT-PCR) assay in two sets from a cohort of 73 brucellosis patients and 65 controls. Results Illumina SBS technology results showed that seven piRNAs were markedly elevated in brucellosis patients compared to normal controls. The seven upregulated piRNAs were further validated individually by qRT-PCR, of which three piRNAs (piR-000753, piR-001312, and piR-016742) were confirmed to be significantly and steadily increased in the patients (> 2-fold, P < 0.01). The area under the receiver operating characteristic (ROC) curve (AUCs) for the three piRNAs ranged from 0.698 to 0.783. The AUC for the three piRNAs combination was 0.772, with a specificity of 86% and a positive predictive value of 90%, respectively. Conclusions The three-piRNA panel identified in this study has potential as a novel blood-based auxiliary tool for brucellosis detection.
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Affiliation(s)
- Cheng Wang
- Department of Clinical Laboratory, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science, NJU Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University, Nanjing, China
- Nanjing Drum Tower Hospital Center of Molecular Diagnostic and Therapy, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute of Life Sciences (NAILS), Institute of Artificial Intelligence Biomedicine, School of Life Sciences, Nanjing University, Nanjing, China
| | - Cuiping Zhang
- Department of Clinical Laboratory, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science, NJU Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University, Nanjing, China
- Nanjing Drum Tower Hospital Center of Molecular Diagnostic and Therapy, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute of Life Sciences (NAILS), Institute of Artificial Intelligence Biomedicine, School of Life Sciences, Nanjing University, Nanjing, China
- Department of Prenatal Diagnosis, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Quan Fu
- Department of Microbiology, Harbin Medical University, Harbin, China
- Department of Clinical Laboratory, Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
| | - Nan Zhang
- Department of Clinical Laboratory, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science, NJU Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University, Nanjing, China
| | - Meng Ding
- Department of Clinical Laboratory, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science, NJU Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University, Nanjing, China
- Nanjing Drum Tower Hospital Center of Molecular Diagnostic and Therapy, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute of Life Sciences (NAILS), Institute of Artificial Intelligence Biomedicine, School of Life Sciences, Nanjing University, Nanjing, China
| | - Zhen Zhou
- Nanjing Drum Tower Hospital Center of Molecular Diagnostic and Therapy, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute of Life Sciences (NAILS), Institute of Artificial Intelligence Biomedicine, School of Life Sciences, Nanjing University, Nanjing, China
| | - Xi Chen
- Nanjing Drum Tower Hospital Center of Molecular Diagnostic and Therapy, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute of Life Sciences (NAILS), Institute of Artificial Intelligence Biomedicine, School of Life Sciences, Nanjing University, Nanjing, China
| | - Fengmin Zhang
- Department of Microbiology, Harbin Medical University, Harbin, China
| | - Chunni Zhang
- Department of Clinical Laboratory, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science, NJU Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University, Nanjing, China
- Nanjing Drum Tower Hospital Center of Molecular Diagnostic and Therapy, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute of Life Sciences (NAILS), Institute of Artificial Intelligence Biomedicine, School of Life Sciences, Nanjing University, Nanjing, China
- *Correspondence: Jun-Jun Wang, ; Chunni Zhang, ; Chen-Yu Zhang,
| | - Chen-Yu Zhang
- Department of Clinical Laboratory, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science, NJU Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University, Nanjing, China
- Nanjing Drum Tower Hospital Center of Molecular Diagnostic and Therapy, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute of Life Sciences (NAILS), Institute of Artificial Intelligence Biomedicine, School of Life Sciences, Nanjing University, Nanjing, China
- *Correspondence: Jun-Jun Wang, ; Chunni Zhang, ; Chen-Yu Zhang,
| | - Jun-Jun Wang
- Department of Clinical Laboratory, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science, NJU Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University, Nanjing, China
- Nanjing Drum Tower Hospital Center of Molecular Diagnostic and Therapy, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute of Life Sciences (NAILS), Institute of Artificial Intelligence Biomedicine, School of Life Sciences, Nanjing University, Nanjing, China
- *Correspondence: Jun-Jun Wang, ; Chunni Zhang, ; Chen-Yu Zhang,
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Deep N-terminomics of Mycobacterium tuberculosis H37Rv extensively correct annotated encoding genes. Genomics 2021; 114:292-304. [PMID: 34915127 DOI: 10.1016/j.ygeno.2021.12.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 11/28/2021] [Accepted: 12/09/2021] [Indexed: 11/24/2022]
Abstract
Mycobacterium tuberculosis (MTB) is a severe causing agent of tuberculosis (TB). Although H37Rv, the type strain of M. tuberculosis was sequenced in 1998, annotation errors of encoding genes have been frequently reported in hundreds of papers. This phenomenon is particularly severe at the 5' end of the genes. Here, we applied a TMPP [(N-Succinimidyloxycarbonylmethyl) tris (2,4,6-trimethoxyphenyl) phosphonium bromide] labeling combined with StageTip separating strategy on M. tuberculosis H37Rv to characterize the N-terminal start sites of its annotated encoding genes. Totally, 1047 proteins were identified with 2058 TMPP labeled N-terminal peptides from all the 2625 mass spectrometer (MS) sequenced proteins. Comparative genomics analysis allowed the re-annotation of 43 proteins' N-termini in H37Rv and 762 proteins in Mycobacteriaceae. All revised N-termini start sites were distributed in 5'-UTR of annotated genes due to over-annotation of previous N-terminal initiation codon, especially the ATG. In addition, we identified and verified a novel gene Rv1078A in +3 frame different from the annotated gene Rv1078 in +2 frame. Altogether, our findings contribute to the better understanding of N-terminal of H37Rv and other species from Mycobacteriaceae that can assist future studies on biological study.
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Yang J, He C, Zhang H, Liu M, Zhao H, Ren L, Wu D, Du F, Liu B, Han X, He S, Chen Z. Evaluation and Differential Diagnosis of a Genetic Marked Brucella Vaccine A19ΔvirB12 for Cattle. Front Immunol 2021; 12:679560. [PMID: 34163479 PMCID: PMC8215367 DOI: 10.3389/fimmu.2021.679560] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 05/10/2021] [Indexed: 01/23/2023] Open
Abstract
Brucella abortus is an important zoonotic pathogen that causes severe economic loss to husbandry and poses a threat to human health. The B. abortus A19 live vaccine has been extensively used to prevent bovine brucellosis in China. However, it is difficult to distinguish the serological response induced by A19 from that induced by natural infection. In this study, a novel genetically marked vaccine, A19ΔvirB12, was generated and evaluated. The results indicated that A19ΔvirB12 was able to provide effective protection against B. abortus 2308 (S2308) challenge in mice. Furthermore, the safety and protective efficacy of A19ΔvirB12 have been confirmed in natural host cattle. Additionally, the VirB12 protein allowed for serological differentiation between the S2308 challenge/natural infection and A19ΔvirB12 vaccination. However, previous studies have found that the accuracy of the serological detection based on VirB12 needs to be improved. Therefore, we attempted to identify potential supplementary antigens with differential diagnostic functions by combining label-free quantitative proteomics and protein chip technology. Twenty-six proteins identified only in S2308 were screened; among them, five proteins were considered as potential supplementary antigens. Thus, the accuracy of the differential diagnosis between A19ΔvirB12 immunization and field infection may be improved through multi-antigen detection. In addition, we explored the possible attenuation factors of Brucella vaccine strain. Nine virulence factors were downregulated in A19ΔvirB12. The downregulation pathways of A19ΔvirB12 were significantly enriched in quorum sensing, ATP-binding cassette transporter, and metabolism. Several proteins related to cell division were significantly downregulated, while some proteins involved in transcription were upregulated in S2308. In conclusion, our results contribute to the control and eradication of brucellosis and provide insights into the mechanisms underlying the attenuation of A19ΔvirB12.
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Affiliation(s)
- Jianghua Yang
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Chuanyu He
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China.,Tecon Biological Co. Ltd., Urumqi, China
| | - Huan Zhang
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | | | | | - Lisong Ren
- Tecon Biological Co. Ltd., Urumqi, China
| | | | - Fangyuan Du
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Baoshan Liu
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Xiaohu Han
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Sun He
- Tecon Biological Co. Ltd., Urumqi, China
| | - Zeliang Chen
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China.,Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, China.,Brucellosis Prevention and Treatment Engineering Technology Research Center of Inner Mongolia Autonomous Region, Inner Mongolia University for Nationalities, Tongliao, China.,School of Public Health, Sun Yat-sen University, Guangzhou, China
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Karevan G, Ahmadi K, Taheri RA, Fasihi-Ramandi M. Immunogenicity of glycine nanoparticles containing a chimeric antigen as Brucella vaccine candidate. Clin Exp Vaccine Res 2021; 10:35-43. [PMID: 33628752 PMCID: PMC7892938 DOI: 10.7774/cevr.2021.10.1.35] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 06/25/2020] [Accepted: 07/28/2020] [Indexed: 12/12/2022] Open
Abstract
Purpose Brucellosis as a worldwide zoonotic illness affect domestic animals and humans doesn't have any vaccine for the prevention of infection in humans yet. The aim of this study was to evaluate the specific immune response following the administration of glycine nanoparticles as adjuvant and delivery system of a chimeric antigen contained trigger factor, Omp31, and Bp26 in murine model. Materials and Methods The chimeric antigen of Brucella was cloned and expressed in Escherichia coli (E. coli) BL21 (DE3). Purification and characterization of recombinant protein was conducted through Ni-NTA (nickel-nitrilotriacetic acid) agarose, SDS-PAGE (sodium dodecyl sulfate-polyacrylamide gel electrophoresis), and Western blot. Nanoparticle characteristics including morphology, particle size distribution, zeta potential, protein retention rate, and release rate were measured in vitro. Subsequently, nanoparticle contained antigen was administered to mice and blood sample was taken to measured the antibody level. Results The protein retention in the nanoparticles was successfully done and the nanoparticle characteristics were appropriate. The average size of glycine particles containing antigen was about 174 nm, and the absorption of protein was approximately 61.27% of the initial value, with a release rate of approximately 70% after 8 hours. Enzyme-linked immunosorbent assay result proved that the immunized sera of mice which were administered with nano-formula contains high levels of antibodies (immunoglobulin G) against recombinant chimeric antigen and also a high level of mucosal antibody (immunoglobulin A) in the oral group, which showed a desirable immunity against Brucella. Conclusion The results showed that chimeric antigen-loaded glycine nanoparticles can act as a vaccine candidate for inducing the cellular and humoral immune response against brucellosis.
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Affiliation(s)
- Ghazal Karevan
- Department of Biology, Nourdanesh Institute of Higher Education, Meymeh, Iran
| | - Kazem Ahmadi
- Molecular Biology Research Center, System Biology and Poisoning Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Ramezan Ali Taheri
- Nanobiotechnology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Mahdi Fasihi-Ramandi
- Molecular Biology Research Center, System Biology and Poisoning Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
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Yang M, Zhu Z, Zhuang Z, Bai Y, Wang S, Ge F. Proteogenomic Characterization of the Pathogenic Fungus Aspergillus flavus Reveals Novel Genes Involved in Aflatoxin Production. Mol Cell Proteomics 2020; 20:100013. [PMID: 33568340 PMCID: PMC7950108 DOI: 10.1074/mcp.ra120.002144] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 10/06/2020] [Accepted: 11/24/2020] [Indexed: 12/20/2022] Open
Abstract
Aspergillus flavus (A. flavus), a pathogenic fungus, can produce carcinogenic and toxic aflatoxins that are a serious agricultural and medical threat worldwide. Attempts to decipher the aflatoxin biosynthetic pathway have been hampered by the lack of a high-quality genome annotation for A. flavus. To address this gap, we performed a comprehensive proteogenomic analysis using high-accuracy mass spectrometry data for this pathogen. The resulting high-quality data set confirmed the translation of 8724 previously predicted genes and identified 732 novel proteins, 269 splice variants, 447 single amino acid variants, 188 revised genes. A subset of novel proteins was experimentally validated by RT-PCR and synthetic peptides. Further functional annotation suggested that a number of the identified novel proteins may play roles in aflatoxin biosynthesis and stress responses in A. flavus. This comprehensive strategy also identified a wide range of posttranslational modifications (PTMs), including 3461 modification sites from 1765 proteins. Functional analysis suggested the involvement of these modified proteins in the regulation of cellular metabolic and aflatoxin biosynthetic pathways. Together, we provided a high-quality annotation of A. flavus genome and revealed novel insights into the mechanisms of aflatoxin production and pathogenicity in this pathogen.
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Affiliation(s)
- Mingkun Yang
- School of Life Sciences, and Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, China; State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Zhuo Zhu
- School of Life Sciences, and Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhenhong Zhuang
- School of Life Sciences, and Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Youhuang Bai
- School of Life Sciences, and Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shihua Wang
- School of Life Sciences, and Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, China.
| | - Feng Ge
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.
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Pan-Proteomic Analysis and Elucidation of Protein Abundance among the Closely Related Brucella Species, Brucella abortus and Brucella melitensis. Biomolecules 2020; 10:biom10060836. [PMID: 32486122 PMCID: PMC7355635 DOI: 10.3390/biom10060836] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/30/2020] [Accepted: 05/19/2020] [Indexed: 12/24/2022] Open
Abstract
Brucellosis is a zoonotic infection caused by bacteria of the genus Brucella. The species, B. abortus and B. melitensis, major causative agents of human brucellosis, share remarkably similar genomes, but they differ in their natural hosts, phenotype, antigenic, immunogenic, proteomic and metabolomic properties. In the present study, label-free quantitative proteomic analysis was applied to investigate protein expression level differences. Type strains and field strains were each cultured six times, cells were harvested at a midlogarithmic growth phase and proteins were extracted. Following trypsin digestion, the peptides were desalted, separated by reverse-phase nanoLC, ionized using electrospray ionization and transferred into an linear trap quadrapole (LTQ) Orbitrap Velos mass spectrometer to record full scan MS spectra (m/z 300–1700) and tandem mass spectrometry (MS/MS) spectra of the 20 most intense ions. Database matching with the reference proteomes resulted in the identification of 826 proteins. The Cluster of Gene Ontologies of the identified proteins revealed differences in bimolecular transport and protein synthesis mechanisms between these two strains. Among several other proteins, antifreeze proteins, Omp10, superoxide dismutase and 30S ribosomal protein S14 were predicted as potential virulence factors among the proteins differentially expressed. All mass spectrometry data are available via ProteomeXchange with identifier PXD006348.
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Wareth G, Pletz MW, Neubauer H, Murugaiyan J. Proteomics of Brucella: Technologies and Their Applications for Basic Research and Medical Microbiology. Microorganisms 2020; 8:microorganisms8050766. [PMID: 32443785 PMCID: PMC7285364 DOI: 10.3390/microorganisms8050766] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 05/18/2020] [Accepted: 05/19/2020] [Indexed: 12/26/2022] Open
Abstract
Brucellosis is a global zoonosis caused by Gram-negative, facultative intracellular bacteria of the genus Brucella (B.). Proteomics has been used to investigate a few B. melitensis and B. abortus strains, but data for other species and biovars are limited. Hence, a comprehensive analysis of proteomes will significantly contribute to understanding the enigmatic biology of brucellae. For direct identification and typing of Brucella, matrix-assisted laser desorption ionization - time of flight mass spectrometry (MALDI - TOF MS) has become a reliable tool for routine diagnosis due to its ease of handling, price and sensitivity highlighting the potential of proteome-based techniques. Proteome analysis will also help to overcome the historic but still notorious Brucella obstacles of infection medicine, the lack of safe and protective vaccines and sensitive serologic diagnostic tools by identifying the most efficient protein antigens. This perspective summarizes past and recent developments in Brucella proteomics with a focus on species identification and serodiagnosis. Future applications of proteomics in these fields are discussed.
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Affiliation(s)
- Gamal Wareth
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses, Naumburger Str. 96a, 07743 Jena, Germany;
- Institute for Infectious Diseases and Infection Control, Jena University Hospital, Am Klinikum 1, 07747 Jena, Germany;
- Faculty of Veterinary Medicine, Benha University, Moshtohor, Toukh 13736, Egypt
- Correspondence: ; Tel.: +49-364-1804-2296
| | - Mathias W. Pletz
- Institute for Infectious Diseases and Infection Control, Jena University Hospital, Am Klinikum 1, 07747 Jena, Germany;
| | - Heinrich Neubauer
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses, Naumburger Str. 96a, 07743 Jena, Germany;
| | - Jayaseelan Murugaiyan
- Institute of Animal Hygiene and Environmental Health, Centre for Infectious Medicine, Freie Universität Berlin, Robert-von-Ostertag-Str. 7-13, 14163 Berlin, Germany;
- Department of Biotechnology, SRM University AP, Neerukonda, Mangalagiri, Andhra Pradesh 522502, India
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Abstract
Brucella spp. are Gram negative intracellular bacteria responsible for brucellosis, a worldwide distributed zoonosis. A prominent aspect of the Brucella life cycle is its ability to invade, survive and multiply within host cells. Comprehensive approaches, such as proteomics, have aided in unravelling the molecular mechanisms underlying Brucella pathogenesis. Technological and methodological advancements such as increased instrument performance and multiplexed quantification have broadened the range of proteome studies, enabling new and improved analyses, providing deeper and more accurate proteome coverage. Indeed, proteomics has demonstrated its contribution to key research questions in Brucella biology, i.e., immunodominant proteins, host-cell interaction, stress response, antibiotic targets and resistance, protein secretion. Here, we review the proteomics of Brucella with a focus on more recent works and novel findings, ranging from reconfiguration of the intracellular bacterial proteome and studies on proteomic profiles of Brucella infected tissues, to the identification of Brucella extracellular proteins with putative roles in cell signaling and pathogenesis. In conclusion, proteomics has yielded copious new candidates and hypotheses that require future verification. It is expected that proteomics will continue to be an invaluable tool for Brucella and applications will further extend to the currently ill-explored aspects including, among others, protein processing and post-translational modification.
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Abkar M, Fasihi-Ramandi M, Kooshki H, Lotfi AS. Intraperitoneal immunization with Urease loaded N -trimethyl Chitosan nanoparticles elicits high protection against Brucella melitensis and Brucella abortus infections. Immunol Lett 2018; 199:53-60. [DOI: 10.1016/j.imlet.2018.03.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Revised: 03/02/2018] [Accepted: 03/10/2018] [Indexed: 01/21/2023]
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12
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Zai X, Yang Q, Yin Y, Li R, Qian M, Zhao T, Li Y, Zhang J, Fu L, Xu J, Chen W. Relative Quantitative Proteomic Analysis of Brucella abortus Reveals Metabolic Adaptation to Multiple Environmental Stresses. Front Microbiol 2017; 8:2347. [PMID: 29238329 PMCID: PMC5712581 DOI: 10.3389/fmicb.2017.02347] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 11/15/2017] [Indexed: 11/19/2022] Open
Abstract
Brucella spp. are facultative intracellular pathogens that cause chronic brucellosis in humans and animals. The virulence of Brucella primarily depends on its successful survival and replication in host cells. During invasion of the host tissue, Brucella is simultaneously subjected to a variety of harsh conditions, including nutrient limitation, low pH, antimicrobial defenses, and extreme levels of reactive oxygen species (ROS) via the host immune response. This suggests that Brucella may be able to regulate its metabolic adaptation in response to the distinct stresses encountered during its intracellular infection of the host. An investigation into the differential proteome expression patterns of Brucella grown under the relevant stress conditions may contribute toward a better understanding of its pathogenesis and adaptive response. Here, we utilized a mass spectrometry-based label-free relative quantitative proteomics approach to investigate and compare global proteomic changes in B. abortus in response to eight different stress treatments. The 3 h short-term in vitro single-stress and multi-stress conditions mimicked the in vivo conditions of B. abortus under intracellular infection, with survival rates ranging from 3.17 to 73.17%. The proteomic analysis identified and quantified a total of 2,272 proteins and 74% of the theoretical proteome, thereby providing wide coverage of the B. abortus proteome. By including eight distinct growth conditions and comparing these with a control condition, we identified a total of 1,221 differentially expressed proteins (DEPs) that were significantly changed under the stress treatments. Pathway analysis revealed that most of the proteins were involved in oxidative phosphorylation, ABC transporters, two-component systems, biosynthesis of secondary metabolites, the citrate cycle, thiamine metabolism, and nitrogen metabolism; constituting major response mechanisms toward the reconstruction of cellular homeostasis and metabolic balance under stress. In conclusion, our results provide a better understanding of the global metabolic adaptations of B. abortus associated with distinct environmental stresses. The identification of proteins necessary for stress resistance is crucial toward elucidating the infectious process in order to control brucellosis, and may facilitate the discovery of novel therapeutic targets and effective vaccines.
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Affiliation(s)
- Xiaodong Zai
- Laboratory of Vaccine and Antibody Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Qiaoling Yang
- Laboratory of Vaccine and Antibody Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Ying Yin
- Laboratory of Vaccine and Antibody Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Ruihua Li
- Laboratory of Vaccine and Antibody Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Mengying Qian
- Laboratory of Vaccine and Antibody Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Taoran Zhao
- Laboratory of Vaccine and Antibody Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Yaohui Li
- Laboratory of Vaccine and Antibody Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Jun Zhang
- Laboratory of Vaccine and Antibody Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Ling Fu
- Laboratory of Vaccine and Antibody Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Junjie Xu
- Laboratory of Vaccine and Antibody Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Wei Chen
- Laboratory of Vaccine and Antibody Engineering, Beijing Institute of Biotechnology, Beijing, China
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