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Arenas S, Rivera N, Méndez Casallas FJ, Galvis B. Assessing Diesel Tolerance of Chromobacterium violaceum: Insights from Growth Kinetics, Substrate Utilization, and Implications for Microbial Adaptation. ACS OMEGA 2024; 9:23741-23752. [PMID: 38854507 PMCID: PMC11154896 DOI: 10.1021/acsomega.4c01698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 04/30/2024] [Accepted: 05/09/2024] [Indexed: 06/11/2024]
Abstract
This study aimed to determine the tolerance of Chromobacterium violaceum ATCC 12472 to diesel. The growth of the strain was evaluated through exposure to various diesel concentrations (1, 2.5, 5, 7.5, and 10% v/v), with continuous monitoring of growth via optical density measurements until the death phase was reached. Employing a logistic model, we analyzed the growth kinetics of C. violaceum and compared them with five other models to comprehend substrate utilization dynamics. Our results indicate that optimal bacterial growth occurred at 2.5% (v/v) or 18,125 mg/L diesel, while both higher and lower concentrations manifested inhibitory and increasingly stressful effects. The Aiba model emerged as the most fitting representation of substrate utilization by C. violaceum. In addition, our findings underscore the remarkable diesel tolerance of C. violaceum ATCC 12472, despite the inherently stressful nature of the medium. This study contributes to the understanding of microbial responses to environmental stressors and highlights the pivotal role of the substrate concentration in influencing microbial growth. These insights have implications for bioremediation strategies and enhance our understanding of bacterial ecological resilience in the presence of hydrocarbon pollutants.
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Affiliation(s)
- Sebastián Arenas
- Programa
de Ingeniería ambiental y Sanitaria, Universidad de La Salle, Bogotá 110231, Colombia
| | - Nathaly Rivera
- Programa
de Ingeniería ambiental y Sanitaria, Universidad de La Salle, Bogotá 110231, Colombia
| | | | - Boris Galvis
- Escuela
de Ingeniería de los Recursos Naturales y del Ambiente—EIDENAR, Universidad del Valle, Cali 760042, Colombia
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GeLC-MS-based proteomics of Chromobacterium violaceum: comparison of proteome changes elicited by hydrogen peroxide. Sci Rep 2016; 6:28174. [PMID: 27321545 PMCID: PMC4913304 DOI: 10.1038/srep28174] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 05/31/2016] [Indexed: 01/14/2023] Open
Abstract
Chromobacterium violaceum is a free-living bacillus with several genes that enables it survival under different harsh environments such as oxidative and temperature stresses. Here we performed a label-free quantitative proteomic study to unravel the molecular mechanisms that enable C. violaceum to survive oxidative stress. To achieve this, total proteins extracted from control and C. violaceum cultures exposed during two hours with 8 mM hydrogen peroxide were analyzed using GeLC-MS proteomics. Analysis revealed that under the stress condition, the bacterium expressed proteins that protected it from the damage caused by reactive oxygen condition and decreasing the abundance of proteins responsible for bacterial growth and catabolism. GeLC-MS proteomics analysis provided an overview of the metabolic pathways involved in the response of C. violaceum to oxidative stress ultimately aggregating knowledge of the response of this organism to environmental stress. This study identified approximately 1500 proteins, generating the largest proteomic coverage of C. violaceum so far. We also detected proteins with unknown function that we hypothesize to be part of new mechanisms related to oxidative stress defense. Finally, we identified the mechanism of clustered regularly interspaced short palindromic repeats (CRISPR), which has not yet been reported for this organism.
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Castro D, Cordeiro IB, Taquita P, Eberlin MN, Garcia JS, Souza GHMF, Arruda MAZ, Andrade EV, Filho SA, Crainey JL, Lozano LL, Nogueira PA, Orlandi PP. Proteomic analysis of Chromobacterium violaceum and its adaptability to stress. BMC Microbiol 2015; 15:272. [PMID: 26627076 PMCID: PMC4666173 DOI: 10.1186/s12866-015-0606-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 11/24/2015] [Indexed: 12/15/2022] Open
Abstract
Background Chromobacterium violaceum (C. violaceum) occurs abundantly in a variety of ecosystems, including ecosystems that place the bacterium under stress. This study assessed the adaptability of C. violaceum by submitting it to nutritional and pH stresses and then analyzing protein expression using bi-dimensional electrophoresis (2-DE) and Maldi mass spectrometry. Results Chromobacterium violaceum grew best in pH neutral, nutrient-rich medium (reference conditions); however, the total protein mass recovered from stressed bacteria cultures was always higher than the total protein mass recovered from our reference culture. The diversity of proteins expressed (repressed by the number of identifiable 2-DE spots) was seen to be highest in the reference cultures, suggesting that stress reduces the overall range of proteins expressed by C. violaceum. Database comparisons allowed 43 of the 55 spots subjected to Maldi mass spectrometry to be characterized as containing a single identifiable protein. Stress-related expression changes were noted for C. violaceum proteins related to the previously characterized bacterial proteins: DnaK, GroEL-2, Rhs, EF-Tu, EF-P; MCP, homogentisate 1,2-dioxygenase, Arginine deiminase and the ATP synthase β-subunit protein as well as for the ribosomal protein subunits L1, L3, L5 and L6. The ability of C. violaceum to adapt its cellular mechanics to sub-optimal growth and protein production conditions was well illustrated by its regulation of ribosomal protein subunits. With the exception of the ribosomal subunit L3, which plays a role in protein folding and maybe therefore be more useful in stressful conditions, all the other ribosomal subunit proteins were seen to have reduced expression in stressed cultures. Curiously, C. violeaceum cultures were also observed to lose their violet color under stress, which suggests that the violacein pigment biosynthetic pathway is affected by stress. Conclusions Analysis of the proteomic signatures of stressed C. violaceum indicates that nutrient-starvation and pH stress can cause changes in the expression of the C. violaceum receptors, transporters, and proteins involved with biosynthetic pathways, molecule recycling, energy production. Our findings complement the recent publication of the C. violeaceum genome sequence and could help with the future commercial exploitation of C. violeaceum. Electronic supplementary material The online version of this article (doi:10.1186/s12866-015-0606-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Diogo Castro
- Instituto Leônidas e Maria Deane - ILMD- Fiocruz, 476 Teresina St., 69057-070, Manaus, AM, Brazil. .,Universidade Estadual do Amazonas, 3578 Djalma Batista Av., 69050-010, Manaus, AM, Brazil.
| | - Isabelle Bezerra Cordeiro
- Universidade Estadual de Campinas, Institute of Chemistry, Thomson Mass Spectrometry Laboratory PO and Spectrometry, Sample Preparation and Mechanization Group (GEPAM), 13084-971, Campinas, SP, Brazil. .,Universidade Estadual do Amazonas, 3578 Djalma Batista Av., 69050-010, Manaus, AM, Brazil.
| | - Paula Taquita
- Instituto Leônidas e Maria Deane - ILMD- Fiocruz, 476 Teresina St., 69057-070, Manaus, AM, Brazil.
| | - Marcos Nogueira Eberlin
- Universidade Estadual de Campinas, Institute of Chemistry, Thomson Mass Spectrometry Laboratory PO and Spectrometry, Sample Preparation and Mechanization Group (GEPAM), 13084-971, Campinas, SP, Brazil.
| | - Jerusa Simone Garcia
- Universidade Estadual de Campinas, Institute of Chemistry, Thomson Mass Spectrometry Laboratory PO and Spectrometry, Sample Preparation and Mechanization Group (GEPAM), 13084-971, Campinas, SP, Brazil.
| | | | - Marco Aurélio Zezzi Arruda
- Universidade Estadual de Campinas, Institute of Chemistry, Thomson Mass Spectrometry Laboratory PO and Spectrometry, Sample Preparation and Mechanization Group (GEPAM), 13084-971, Campinas, SP, Brazil.
| | - Edmar V Andrade
- Universidade Estadual do Amazonas, 3578 Djalma Batista Av., 69050-010, Manaus, AM, Brazil.
| | - Spartaco A Filho
- Universidade Estadual do Amazonas, 3578 Djalma Batista Av., 69050-010, Manaus, AM, Brazil.
| | - J Lee Crainey
- Instituto Leônidas e Maria Deane - ILMD- Fiocruz, 476 Teresina St., 69057-070, Manaus, AM, Brazil.
| | - Luis Lopez Lozano
- Biotechnology Laboratory/ Universidade Federal do Amazonas, 3000 Rodrigo Octávio Av., 69077-000, Manaus, AM, Brazil.
| | - Paulo A Nogueira
- Instituto Leônidas e Maria Deane - ILMD- Fiocruz, 476 Teresina St., 69057-070, Manaus, AM, Brazil.
| | - Patrícia P Orlandi
- Instituto Leônidas e Maria Deane - ILMD- Fiocruz, 476 Teresina St., 69057-070, Manaus, AM, Brazil.
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