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Husain AA, Pinto SM, Agarwal N, Behera SK, Khulkhule PR, Bhartiya NM, Subbannayya Y, Prasad TSK, Singh LR, Daginawala HF, Kashyap RS. Comprehensive Proteomic Analysis of Brucella melitensis ATCC23457 Strain Reveals Metabolic Adaptations in Response to Nutrient Stress. Curr Microbiol 2022; 80:20. [PMID: 36460801 DOI: 10.1007/s00284-022-03105-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 10/29/2022] [Indexed: 12/04/2022]
Abstract
In the present study, a comprehensive proteomic analysis of Brucella melitensis (B. melitensis) strain ATCC23457 was carried out to investigate proteome alterations in response to in vitro-induced nutrient stress. Our analysis resulted in the identification of 2440 proteins, including 365 hypothetical proteins and 850 potentially secretory proteins representing ~77.8% of the B. melitensis proteome. Utilizing a proteogenomics approach, we provide translational evidence for eight novel putative protein-coding genes and confirmed the coding potential of 31 putatively annotated pseudogenes, thus refining the existing genome annotation. Further, using a label-free quantitative proteomic approach, new insights into the cellular processes governed by nutrient stress, including enrichment of amino acid metabolism (E), transcription (K), energy production and conversion (C), and biogenesis (J) processes were obtained. Pathway analysis revealed the enrichment of survival and homeostasis maintenance pathways, including type IV secretion system, nitrogen metabolism, and urease pathways in response to nutrient limitation. To conclude, our analysis demonstrates the utility of in-depth proteomic analysis in enabling improved annotation of the B. melitensis genome. Further, our results indicate that B. melitensis undergoes metabolic adaptations during nutrient stress similar to other Brucella. sp, and adapts itself for long-term persistence and survival.
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Affiliation(s)
- Aliabbas A Husain
- Research Center, Dr. G.M. Taori Central India Institute of Medical Sciences (CIIMS), Nagpur, 440 010, India
| | - Sneha M Pinto
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to Be University), Mangalore, 575018, India
| | - Nupur Agarwal
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to Be University), Mangalore, 575018, India
| | - Santosh K Behera
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to Be University), Mangalore, 575018, India
| | - Payal R Khulkhule
- Research Center, Dr. G.M. Taori Central India Institute of Medical Sciences (CIIMS), Nagpur, 440 010, India
| | - Nidhi M Bhartiya
- Research Center, Dr. G.M. Taori Central India Institute of Medical Sciences (CIIMS), Nagpur, 440 010, India
| | - Yashwanth Subbannayya
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to Be University), Mangalore, 575018, India
| | - T S Keshava Prasad
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to Be University), Mangalore, 575018, India.
| | - Lokendra R Singh
- Research Center, Dr. G.M. Taori Central India Institute of Medical Sciences (CIIMS), Nagpur, 440 010, India
| | - Hatim F Daginawala
- Research Center, Dr. G.M. Taori Central India Institute of Medical Sciences (CIIMS), Nagpur, 440 010, India
| | - Rajpal S Kashyap
- Research Center, Dr. G.M. Taori Central India Institute of Medical Sciences (CIIMS), Nagpur, 440 010, India.
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Ling N, Ou D, Shen Y, Zhang D, Wang Y, Tong L, Ding Y, Wang J, Yang X, Zhang J, Wu Q, Ye Y. Proteomics analysis mediated by quorum sensing luxS involved in oxidative stress in Cronobacter malonaticus. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2021.111576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Steinle H, Ellwanger K, Mirza N, Briese S, Kienes I, Pfannstiel J, Kufer TA. 14-3-3 and erlin proteins differentially interact with RIPK2 complexes. J Cell Sci 2021; 134:jcs258137. [PMID: 34152391 DOI: 10.1242/jcs.258137] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 05/19/2021] [Indexed: 01/11/2023] Open
Abstract
The receptor interacting serine/threonine kinase 2 (RIPK2) is essential for signal transduction induced by the pattern recognition receptors NOD1 and NOD2 (referred to collectively as NOD1/2). Upon NOD1/2 activation, RIPK2 forms complexes in the cytoplasm of human cells. Here, we identified the molecular composition of these complexes. Infection with Shigella flexneri to activate NOD1-RIPK2 revealed that RIPK2 formed dynamic interactions with several cellular proteins, including A20 (also known as TNFAIP3), erlin-1, erlin-2 and 14-3-3. Whereas interaction of RIPK2 with 14-3-3 proteins was strongly reduced upon infection with Shigella, erlin-1 and erlin-2 (erlin-1/2) specifically bound to RIPK2 complexes. The interaction of these proteins with RIPK2 was validated using protein binding assays and immunofluorescence staining. Beside bacterial activation of NOD1/2, depletion of the E3 ubiquitin ligase XIAP and treatment with RIPK2 inhibitors also led to the formation of RIPK2 cytosolic complexes. Although erlin-1/2 were recruited to RIPK2 complexes following XIAP inhibition, these proteins did not associate with RIPK2 structures induced by RIPK2 inhibitors. While the specific recruitment of erlin-1/2 to RIPK2 suggests a role in innate immune signaling, the biological response regulated by the erlin-1/2-RIPK2 association remains to be determined.
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Affiliation(s)
- Heidrun Steinle
- Department of Immunology, Institute of Nutritional Medicine, University of Hohenheim, 70619 Stuttgart, Germany
| | - Kornelia Ellwanger
- Department of Immunology, Institute of Nutritional Medicine, University of Hohenheim, 70619 Stuttgart, Germany
| | - Nora Mirza
- Department of Immunology, Institute of Nutritional Medicine, University of Hohenheim, 70619 Stuttgart, Germany
| | - Selina Briese
- Department of Immunology, Institute of Nutritional Medicine, University of Hohenheim, 70619 Stuttgart, Germany
| | - Ioannis Kienes
- Department of Immunology, Institute of Nutritional Medicine, University of Hohenheim, 70619 Stuttgart, Germany
| | - Jens Pfannstiel
- Core Facility Hohenheim Mass Spectrometry Module, Institute of Nutritional Medicine, University of Hohenheim, 70619 Stuttgart, Germany
| | - Thomas A Kufer
- Department of Immunology, Institute of Nutritional Medicine, University of Hohenheim, 70619 Stuttgart, Germany
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Hu S, Yu Y, Lv Z, Shen J, Ke Y, Xiao X. Proteomics study unveils ROS balance in acid-adapted Salmonella Enteritidis. Food Microbiol 2020; 92:103585. [PMID: 32950169 DOI: 10.1016/j.fm.2020.103585] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 06/08/2020] [Accepted: 06/24/2020] [Indexed: 12/21/2022]
Abstract
Salmonella Enteritidis is a major cause of foodborne gastroenteritis and is thus a persistent threat to global public health. The acid adaptation response helps Salmonella survive exposure to gastric environment during ingestion. In a previous study we highlighted the damage caused to cell membrane and the regulation of intracellular reactive oxygen species (ROS) in S. Enteritidis. In this study, we applied both physiologic and iTRAQ analyses to explore the regulatory mechanism of acid resistance in Salmonella. It was found that after S. Enteritidis was subject to a 1 h period of acid adaptation at pH 5.5, an additional 1 h period of acid shock stress at pH 3.0 caused less Salmonella cell death than in non-acid adapted Salmonella cells. Although there were no significant differences between adapted and non-adapted cells in terms of cell membrane damage (e.g., membrane permeability or lipid peroxidation) after 30 min, intracellular ROS level in acid adapted cells was dramatically reduced compared to that in non-acid adapted cells, indicating that acid adaption promoted less ROS generation or increased the ability of ROS scavenging with little reduction in the integrity of the cell membrane. These findings were confirmed via an iTRAQ analysis. The adapted cells were shown to trigger incorporation of exogenous long-chain fatty acids into the cellular membrane, resulting in a different membrane lipid profile and promoting survival rate under acid stress. S. Enteritidis experiences oxidative damage and iron deficiency under acid stress, but after acid adaption S. Enteritidis cells were able to balance their concentrations of intracellular ROS. Specifically, SodAB consumed the free protons responsible for forming reactive oxygen intermediates (ROIs) and KatE protected cells from the toxic effects of ROIs. Additionally, acid-labile proteins released free unbound iron promoting ferroptotic metabolism, and NADH reduced GSSH to G-SH, protecting cells from acid/oxidative stress.
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Affiliation(s)
- Shuangfang Hu
- Key Laboratory of Molecular Epidemiology of Shenzhen, Shenzhen Center for Disease Control and Prevention, Shenzhen City, Guangdong Province, 518055, PR China; School of Food Science and Engineering, South China University of Technology, Guangzhou City, Guangdong Province, 510640, PR China; Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, 10083, PR China
| | - Yigang Yu
- School of Food Science and Engineering, South China University of Technology, Guangzhou City, Guangdong Province, 510640, PR China
| | - Ziquan Lv
- Key Laboratory of Molecular Epidemiology of Shenzhen, Shenzhen Center for Disease Control and Prevention, Shenzhen City, Guangdong Province, 518055, PR China
| | - Jianzhong Shen
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, 10083, PR China
| | - Yuebin Ke
- Key Laboratory of Molecular Epidemiology of Shenzhen, Shenzhen Center for Disease Control and Prevention, Shenzhen City, Guangdong Province, 518055, PR China.
| | - Xinglong Xiao
- School of Food Science and Engineering, South China University of Technology, Guangzhou City, Guangdong Province, 510640, PR China.
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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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Song H, Lei Y, Zhang S. Differences in resistance to nitrogen and phosphorus deficiencies explain male-biased populations of poplar in nutrient-deficient habitats. J Proteomics 2018; 178:123-127. [DOI: 10.1016/j.jprot.2017.11.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 11/06/2017] [Accepted: 11/17/2017] [Indexed: 12/30/2022]
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De Y, Dong C, Cao Y, Wang X, Yang X, Wang N, Zhang C, Wang Z, Lyu Y, Wu Q. Genome-wide sequence transposon insertion sites and analyze the essential genes of Brucella melitensis. Microb Pathog 2017; 112:97-102. [PMID: 28888882 DOI: 10.1016/j.micpath.2017.09.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 09/03/2017] [Accepted: 09/05/2017] [Indexed: 12/29/2022]
Abstract
A transposon mutant library of B. melitensis NI including 32,640 transposon mutants was established. By sequencing the transposon insertion sites, 10,832 mutants were successfully defined for their insertion sites. Analysis of the mutants with defined transposon insertion sites (DTIS) indicated that the insertions were well spread through the two genomes. In addition, 948 genes with no detectable transposon insertions were taken as the candidate for identification of essential genes. In comparison with the Bacterial Database of Essential Genes and by using comparative genomics analysis, 183 potential essential genes of B. melitensis NI cultured in vitro were found and they were conserved in the common bacteria. This work was focused on screening of the essential genes of B. melitensis NI, which may provide a foundation for identification of the novel drug targets against brucellosis. Besides, the sequence-defined transposon library should serve as a resource for screening of different function genes of Brucella.
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Affiliation(s)
- Yanyan De
- Key Laboratory of Animal Epidemiology and Zoonosis of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Congyue Dong
- Key Laboratory of Animal Epidemiology and Zoonosis of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Yanyang Cao
- Key Laboratory of Animal Epidemiology and Zoonosis of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Xiaolei Wang
- Key Laboratory of Animal Epidemiology and Zoonosis of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Xiaowen Yang
- Key Laboratory of Animal Epidemiology and Zoonosis of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Ning Wang
- Key Laboratory of Animal Epidemiology and Zoonosis of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Cunrui Zhang
- Key Laboratory of Animal Epidemiology and Zoonosis of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Zhen Wang
- Key Laboratory of Animal Epidemiology and Zoonosis of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Yanli Lyu
- Key Laboratory of Animal Epidemiology and Zoonosis of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Qingmin Wu
- Key Laboratory of Animal Epidemiology and Zoonosis of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China.
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Comparative proteomic analysis of Cronobacter sakazakii by iTRAQ provides insights into response to desiccation. Food Res Int 2017; 100:631-639. [PMID: 28873731 DOI: 10.1016/j.foodres.2017.06.051] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 06/18/2017] [Accepted: 06/20/2017] [Indexed: 11/21/2022]
Abstract
Cronobacter sakazakii is a foodborne pathogen throughout the world and survives extremely desiccation stress. However, the molecular basis involved in desiccation resistance of C. sakazakii is still unknown. In this study, the potential desiccation resistance factors of C. sakazakii ATCC 29544 were determined using iTRAQ-based quantitative proteomic analysis. A total of 2775 proteins were identified by iTRAQ, of which 233 showed a different protein expression between control group and desiccation stress group. Among these 233 proteins identified as desiccation resistance proteins, there were 146 proteins downregulated and 87 proteins upregulated. According to the comprehensive proteome coverage analysis, C. sakazakii increased its resistance to desiccation by reducing the gene involved with unnecessary survival functions such as those used for virulence, adhesion, invasion and flagella assembly, while increasing gene expression of genes used in withstanding osmotic stress such as those genes involved in trehalose and betaine uptake. However, the mechanism involved in amino acid metabolism in an osmotic stress response, including the producing of γ-aminobutyric acid in C. sakazakii is still uncertain. This is the first report to determine the potential desiccation resistant factors of C. sakazakii at the proteomic levels.
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Mol JPS, Pires SF, Chapeaurouge AD, Perales J, Santos RL, Andrade HM, Lage AP. Proteomic Profile of Brucella abortus-Infected Bovine Chorioallantoic Membrane Explants. PLoS One 2016; 11:e0154209. [PMID: 27104343 PMCID: PMC4841507 DOI: 10.1371/journal.pone.0154209] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 04/11/2016] [Indexed: 12/20/2022] Open
Abstract
Brucella abortus is the etiological agent of bovine brucellosis, a zoonotic disease that causes significant economic losses worldwide. The differential proteomic profile of bovine chorioallantoic membrane (CAM) explants at early stages of infection with B. abortus (0.5, 2, 4, and 8 h) was determined. Analysis of CAM explants at 0.5 and 4 h showed the highest differences between uninfected and infected CAM explants, and therefore were used for the Differential Gel Electrophoresis (DIGE). A total of 103 spots were present in only one experimental group and were selected for identification by mass spectrometry (MALDI/ToF-ToF). Proteins only identified in extracts of CAM explants infected with B. abortus were related to recognition of PAMPs by TLR, production of reactive oxygen species, intracellular trafficking, and inflammation.
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Affiliation(s)
- Juliana P. S. Mol
- Universidade Federal de Minas Gerais, Escola de Veterinária, Departamento de Medicina Veterinária Preventiva, Belo Horizonte, Minas Gerais, Brazil
| | - Simone F. Pires
- Universidade Federal de Minas Gerais, Instituto de Ciências Biológicas, Departamento de Parasitologia, Belo Horizonte, Minas Gerais, Brazil
| | - Alexander D. Chapeaurouge
- Fundação Oswaldo Cruz, Instituto Oswaldo Cruz, Laboratório de Toxinologia, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Jonas Perales
- Fundação Oswaldo Cruz, Instituto Oswaldo Cruz, Laboratório de Toxinologia, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Renato L. Santos
- Universidade Federal de Minas Gerais, Escola de Veterinária, Departamento de Clínica e Cirurgia Veterinárias, Minas Gerais, Brasil
| | - Hélida M. Andrade
- Universidade Federal de Minas Gerais, Instituto de Ciências Biológicas, Departamento de Parasitologia, Belo Horizonte, Minas Gerais, Brazil
| | - Andrey P. Lage
- Universidade Federal de Minas Gerais, Escola de Veterinária, Departamento de Medicina Veterinária Preventiva, Belo Horizonte, Minas Gerais, Brazil
- * E-mail:
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