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Rijal R, Gomer RH. Gallein potentiates isoniazid's ability to suppress Mycobacterium tuberculosis growth. Front Microbiol 2024; 15:1369763. [PMID: 38690363 PMCID: PMC11060752 DOI: 10.3389/fmicb.2024.1369763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 04/01/2024] [Indexed: 05/02/2024] Open
Abstract
Mycobacterium tuberculosis (Mtb), the bacterium that causes tuberculosis (TB), can be difficult to treat because of drug tolerance. Increased intracellular polyphosphate (polyP) in Mtb enhances tolerance to antibiotics, and capsular polyP in Neisseria gonorrhoeae potentiates resistance to antimicrobials. The mechanism by which bacteria utilize polyP to adapt to antimicrobial pressure is not known. In this study, we found that Mtb adapts to the TB frontline antibiotic isoniazid (INH) by enhancing the accumulation of cellular, extracellular, and cell surface polyP. Gallein, a broad-spectrum inhibitor of the polyphosphate kinase that synthesizes polyP, prevents this INH-induced increase in extracellular and cell surface polyP levels. Gallein and INH work synergistically to attenuate Mtb's ability to grow in in vitro culture and within human macrophages. Mtb when exposed to INH, and in the presence of INH, gallein inhibits cell envelope formation in most but not all Mtb cells. Metabolomics indicated that INH or gallein have a modest impact on levels of Mtb metabolites, but when used in combination, they significantly reduce levels of metabolites involved in cell envelope synthesis and amino acid, carbohydrate, and nucleoside metabolism, revealing a synergistic effect. These data suggest that gallein represents a promising avenue to potentiate the treatment of TB.
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Affiliation(s)
- Ramesh Rijal
- Gomer Lab, Department of Biology, Texas A&M University, College Station, TX, United States
| | - Richard H. Gomer
- Gomer Lab, Department of Biology, Texas A&M University, College Station, TX, United States
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2
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Rijal R, Gomer RH. Gallein and isoniazid act synergistically to attenuate Mycobacterium tuberculosis growth in human macrophages. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.10.574965. [PMID: 38260681 PMCID: PMC10802476 DOI: 10.1101/2024.01.10.574965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Mycobacterium tuberculosis (Mtb), the bacterium that causes tuberculosis (TB), can be difficult to treat because of drug resistance. Increased intracellular polyphosphate (polyP) in Mtb enhances resistance to antibiotics, and capsular polyP in Neisseria gonorrhoeae potentiates resistance to antimicrobials. The mechanism by which bacteria utilize polyP to adapt to antimicrobial pressure is not known. In this study, we found that Mtb adapts to the TB frontline antibiotic isoniazid (INH) by enhancing the accumulation of cellular, extracellular, and cell surface polyP. Gallein, a broad-spectrum inhibitor of the polyphosphate kinase that synthesizes polyP, prevents this INH-induced increase in extracellular and cell surface polyP levels. Gallein and INH work synergistically to attenuate Mtb's ability to grow in in vitro culture and within human macrophages. Mtb when exposed to INH, and in the presence of INH, gallein inhibits cell envelope formation in most but not all Mtb cells. Metabolomics indicated that INH or gallein have a modest impact on levels of Mtb metabolites, but when used in combination, they significantly reduce levels of metabolites involved in cell envelope synthesis and amino acid, carbohydrate, and nucleoside metabolism, revealing a synergistic effect. These data suggest that gallein represents a promising avenue to potentiate the treatment of TB.
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Affiliation(s)
- Ramesh Rijal
- Department of Biology, Texas A&M University, College Station, TX 77843-3474, USA
| | - Richard H. Gomer
- Department of Biology, Texas A&M University, College Station, TX 77843-3474, USA
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3
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Lobo CB, Correa Deza MA, Arnau GV, Ferrero MA, Juárez Tomás MS. Dibenzothiophene removal by environmental bacteria with differential accumulation of intracellular inorganic polyphosphate. BIORESOURCE TECHNOLOGY 2023; 387:129582. [PMID: 37506945 DOI: 10.1016/j.biortech.2023.129582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/24/2023] [Accepted: 07/25/2023] [Indexed: 07/30/2023]
Abstract
Dibenzothiophene (DBT), which belongs to the group of polycyclic aromatic heterocycles of sulfur, is a model substance to study the removal of sulfur compounds from oil due to its recalcitrance to traditional and specific removal processes. The aim of this work was to evaluate DBT bioremoval by environmental bacteria and its relationship with polyphosphate (polyP) accumulation, cell surface characteristics and bioemulsifying activity. Pseudomonas sp. P26 achieved the highest DBT removal percentage (48%) after 7 days of incubation. Moreover, positive correlations were estimated between DBT removal and bioemulsifying activity and biofilm formation. A strain-dependent relationship between the content of intracellular polyP and the presence of DBT in the culture medium was also demonstrated. The study of these bacterial characteristics, which could promote DBT transformation, is a first approach to select DBT-removing bacteria, in order to develop bioformulations that are able to contribute to desulfurization processes of petroleum-derived pollutants in the future.
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Affiliation(s)
- Constanza Belén Lobo
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), Av. Belgrano y Pje. Caseros, San Miguel de Tucumán (T4001MVB), Tucumán, Argentina.
| | - María Alejandra Correa Deza
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), Av. Belgrano y Pje. Caseros, San Miguel de Tucumán (T4001MVB), Tucumán, Argentina.
| | - Gonzalo Víctor Arnau
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), Av. Belgrano y Pje. Caseros, San Miguel de Tucumán (T4001MVB), Tucumán, Argentina.
| | - Marcela Alejandra Ferrero
- YPF Tecnología (Y-TEC), Av. del Petróleo Argentino (RP10) S/N entre 129 y 143 (1923), Berisso, Buenos Aires, Argentina.
| | - María Silvina Juárez Tomás
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), Av. Belgrano y Pje. Caseros, San Miguel de Tucumán (T4001MVB), Tucumán, Argentina.
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4
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Yu F, Luo W, Xie W, Li Y, Liu Y, Ye X, Peng T, Wang H, Huang T, Hu Z. The effects of long-term hexabromocyclododecanes contamination on microbial communities in the microcosms. CHEMOSPHERE 2023; 325:138412. [PMID: 36925001 DOI: 10.1016/j.chemosphere.2023.138412] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 01/21/2023] [Accepted: 03/13/2023] [Indexed: 06/18/2023]
Abstract
The adaptation of microbial community to the long-term contamination of hexabromocyclododecanes (HBCDs) has not been well studied. Our previous study found that the HBCDs contamination in the microcosms constructed of sediments from two different mangrove forests in 8 months resulted in serious acidification (pH2-3). This study reanalyzed previous sequencing data and compared them with data after 20 months to investigate the adaptive properties of microbial communities in the stress of HBCDs and acidification. It hypothesized that the reassembly was based on the fitness of taxa. The results indicated that eukaryotes and fungi might have better adaptive capacity to these deteriorated habitats. Eukaryotic taxa Eufallia and Syncystis, and fungal taxa Wickerhamomyces were only detected after 20 months of contamination. Moreover, eukaryotic taxa Caloneis and Nitzschia, and fungal taxa Talaromyces were dominant in most of microbial communities (14.467-95.941%). The functional compositions were sediment-dependent and more divergent than community reassemblies. Network and co-occurrence analysis suggested that acidophiles such as Acidisoma and Acidiphilium were gaining more positive relations in the long-term stress. The acidophilic taxa and genes involved in resistance to the acidification and toxicity of HBCDs were enriched, for example, bacteria Acidisoma and Acidiphilium, archaea Thermogymnomonas, and eukaryotes Nitzschia, and genes kdpC, odc1, polA, gst, and sod-2. These genes involved in oxidative stress response, energy metabolism, DNA damage repair, potassium transportation, and decarboxylation. It suggested that the microbial communities might cope with the stress from HBCDs and acidification via multiple pathways. The present research shed light on the evolution of microbial communities under the long-term stress of HBCDs contamination and acidification.
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Affiliation(s)
- Fei Yu
- Department of Biology, College of Science, Shantou University, Shantou, Guangdong Province, China
| | - Wenqi Luo
- Department of Biology, College of Science, Shantou University, Shantou, Guangdong Province, China
| | - Wei Xie
- Department of Biology, College of Science, Shantou University, Shantou, Guangdong Province, China
| | - Yuyang Li
- Department of Biology, College of Science, Shantou University, Shantou, Guangdong Province, China
| | - Yongjin Liu
- Department of Biology, College of Science, Shantou University, Shantou, Guangdong Province, China
| | - Xueying Ye
- Department of Biology, College of Science, Shantou University, Shantou, Guangdong Province, China
| | - Tao Peng
- Department of Biology, College of Science, Shantou University, Shantou, Guangdong Province, China
| | - Hui Wang
- Department of Biology, College of Science, Shantou University, Shantou, Guangdong Province, China
| | - Tongwang Huang
- Department of Biology, College of Science, Shantou University, Shantou, Guangdong Province, China.
| | - Zhong Hu
- Department of Biology, College of Science, Shantou University, Shantou, Guangdong Province, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong Province, China.
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5
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Exopolyphosphatases PPX1 and PPX2 from Mycobacterium tuberculosis regulate dormancy response and pathogenesis. Microb Pathog 2022; 173:105885. [DOI: 10.1016/j.micpath.2022.105885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 11/12/2022] [Accepted: 11/12/2022] [Indexed: 11/21/2022]
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6
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Tracing Carbon Metabolism with Stable Isotope Metabolomics Reveals the Legacy of Diverse Carbon Sources in Soil. Appl Environ Microbiol 2022; 88:e0083922. [PMID: 36300927 PMCID: PMC9680644 DOI: 10.1128/aem.00839-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Carbon metabolism in soil remains poorly described due to the inherent difficulty of obtaining information on the microbial metabolites produced by complex soil communities. Our study demonstrates the use of stable isotope probing (SIP) to study carbon metabolism in soil by tracking
13
C from supplied carbon sources into metabolite pools and biomass.
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Bopp CE, Bernet NM, Kohler HPE, Hofstetter TB. Elucidating the Role of O 2 Uncoupling in the Oxidative Biodegradation of Organic Contaminants by Rieske Non-heme Iron Dioxygenases. ACS ENVIRONMENTAL AU 2022; 2:428-440. [PMID: 36164353 PMCID: PMC9502038 DOI: 10.1021/acsenvironau.2c00023] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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Oxygenations of aromatic
soil and water contaminants with molecular
O2 catalyzed by Rieske dioxygenases are frequent initial
steps of biodegradation in natural and engineered environments. Many
of these non-heme ferrous iron enzymes are known to be involved in
contaminant metabolism, but the understanding of enzyme–substrate
interactions that lead to successful biodegradation is still elusive.
Here, we studied the mechanisms of O2 activation and substrate
hydroxylation of two nitroarene dioxygenases to evaluate enzyme- and
substrate-specific factors that determine the efficiency of oxygenated
product formation. Experiments in enzyme assays of 2-nitrotoluene
dioxygenase (2NTDO) and nitrobenzene dioxygenase (NBDO) with methyl-,
fluoro-, chloro-, and hydroxy-substituted nitroaromatic substrates
reveal that typically 20–100% of the enzyme’s activity
involves unproductive paths of O2 activation with generation
of reactive oxygen species through so-called O2 uncoupling.
The 18O and 13C kinetic isotope effects of O2 activation and nitroaromatic substrate hydroxylation, respectively,
suggest that O2 uncoupling occurs after generation of FeIII-(hydro)peroxo species in the catalytic cycle. While 2NTDO
hydroxylates ortho-substituted nitroaromatic substrates
more efficiently, NBDO favors meta-substituted, presumably
due to distinct active site residues of the two enzymes. Our data
implies, however, that the O2 uncoupling and hydroxylation
activity cannot be assessed from simple structure–reactivity
relationships. By quantifying O2 uncoupling by Rieske dioxygenases,
our work provides a mechanistic link between contaminant biodegradation,
the generation of reactive oxygen species, and possible adaptation
strategies of microorganisms to the exposure of new contaminants.
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Affiliation(s)
- Charlotte E. Bopp
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zürich, 8092 Zürich, Switzerland
| | - Nora M. Bernet
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
| | - Hans-Peter E. Kohler
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
| | - Thomas B. Hofstetter
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zürich, 8092 Zürich, Switzerland
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Solar Venero EC, Matera G, Vogel J, López NI, Tribelli PM. Small RNAs in the Antarctic bacterium Pseudomonas extremaustralis responsive to oxygen availability and oxidative stress. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:604-615. [PMID: 35689330 DOI: 10.1111/1758-2229.13084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Accepted: 05/07/2022] [Indexed: 06/15/2023]
Abstract
Bacterial small non-coding RNAs (sRNAs) play key roles as genetic regulators, mediating in the adaptability to changing environmental conditions and stress responses. In this work, we analysed putative sRNAs identified by RNA-seq experiments in different aeration conditions in the extremophile bacterium P. extremaustralis. These analyses allowed the identification of 177 putative sRNAs under aerobiosis (A), microaerobiosis (M) and microaerobiosis after H2 O2 exposure (m-OS). The size and transcription profile of eight sRNAs with differential expression were verified by Northern blot. sRNA40, with unknown function but conserved in other Pseudomonas species, was selected to perform overexpression experiments followed by RNA-seq analysis. The overexpression of sRNA40 in P. extremaustralis resulted in significant expression changes of 19 genes with 14 differentially upregulated and five downregulated. Among the upregulated genes, eight transcripts corresponded to components of secretion systems, such as gspH, gspK, and gspM, belonging to the Type II secretion system, and rspO and rspP from Type III secretion system. Our results showed a novel sRNA which expression was triggered by low oxygen levels, and whose overexpression was associated with upregulation of selected components of protein secretion systems.
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Affiliation(s)
| | - Gianluca Matera
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, Würzburg, Germany
| | - Jörg Vogel
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, Würzburg, Germany
| | - Nancy I López
- IQUIBICEN-CONICET, Intendente Guiraldes 2160, 1428EGA, Buenos Aires, Argentina
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, 1428EGA, Buenos Aires, Argentina
| | - Paula M Tribelli
- IQUIBICEN-CONICET, Intendente Guiraldes 2160, 1428EGA, Buenos Aires, Argentina
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, 1428EGA, Buenos Aires, Argentina
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9
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Salicylate or Phthalate: The Main Intermediates in the Bacterial Degradation of Naphthalene. Processes (Basel) 2021. [DOI: 10.3390/pr9111862] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are widely presented in the environment and pose a serious environmental threat due to their toxicity. Among PAHs, naphthalene is the simplest compound. Nevertheless, due to its high toxicity and presence in the waste of chemical and oil processing industries, naphthalene is one of the most critical pollutants. Similar to other PAHs, naphthalene is released into the environment via the incomplete combustion of organic compounds, pyrolysis, oil spills, oil processing, household waste disposal, and use of fumigants and deodorants. One of the main ways to detoxify such compounds in the natural environment is through their microbial degradation. For the first time, the pathway of naphthalene degradation was investigated in pseudomonades. The salicylate was found to be a key intermediate. For some time, this pathway was considered the main, if not the only one, in the bacterial destruction of naphthalene. However, later, data emerged which indicated that gram-positive bacteria in the overwhelming majority of cases are not capable of the formation/destruction of salicylate. The obtained data made it possible to reveal that protocatechoate, phthalate, and cinnamic acids are predominant intermediates in the destruction of naphthalene by rhodococci. Pathways of naphthalene degradation, the key enzymes, and genetic regulation are the main subjects of the present review, representing an attempt to summarize the current knowledge about the mechanism of the microbial degradation of PAHs. Modern molecular methods are also discussed in the context of the development of “omics” approaches, namely genomic, metabolomic, and proteomic, used as tools for studying the mechanisms of microbial biodegradation. Lastly, a comprehensive understanding of the mechanisms of the formation of specific ecosystems is also provided.
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10
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Moriuchi R, Dohra H, Kanesaki Y, Ogawa N. Transcriptome differences between Cupriavidus necator NH9 grown with 3-chlorobenzoate and that grown with benzoate. Biosci Biotechnol Biochem 2021; 85:1546-1561. [PMID: 33720310 DOI: 10.1093/bbb/zbab044] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 03/08/2021] [Indexed: 01/05/2023]
Abstract
RNA-seq analysis of Cupriavidus necator NH9, a 3-chlorobenzoate degradative bacterium, cultured with 3-chlorobenzaote and benzoate, revealed strong induction of genes encoding enzymes in degradation pathways of the respective compound, including the genes to convert 3-chlorobenzaote and benzoate to chlorocatechol and catechol, respectively, and the genes of chlorocatechol ortho-cleavage pathway for conversion to central metabolites. The genes encoding transporters, components of the stress response, flagellar proteins, and chemotaxis proteins showed altered expression patterns between 3-chlorobenzoate and benzoate. Gene Ontology enrichment analysis revealed that chemotaxis-related terms were significantly upregulated by benzoate compared with 3-chlorobenzoate. Consistent with this, in semisolid agar plate assays, NH9 cells showed stronger chemotaxis to benzoate than to 3-chlorobenzoate. These results, combined with the absence of genes related to uptake/chemotaxis for 3-chlorobenzoate located closely to the degradation genes of 3-chlorobenzoate, suggested that NH9 has not fully adapted to the utilization of chlorinated benzoate, unlike benzoate, in nature.
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Affiliation(s)
- Ryota Moriuchi
- Research Institute of Green Science and Technology, Shizuoka University, Shizuoka-shi, Shizuoka, Japan.,The United Graduate School of Agricultural Science, Gifu University, Gifu-shi, Gifu, Japan
| | - Hideo Dohra
- Research Institute of Green Science and Technology, Shizuoka University, Shizuoka-shi, Shizuoka, Japan
| | - Yu Kanesaki
- Research Institute of Green Science and Technology, Shizuoka University, Shizuoka-shi, Shizuoka, Japan
| | - Naoto Ogawa
- The United Graduate School of Agricultural Science, Gifu University, Gifu-shi, Gifu, Japan.,Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka-shi, Shizuoka, Japan
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11
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Pátek M, Grulich M, Nešvera J. Stress response in Rhodococcus strains. Biotechnol Adv 2021; 53:107698. [PMID: 33515672 DOI: 10.1016/j.biotechadv.2021.107698] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 01/13/2021] [Accepted: 01/15/2021] [Indexed: 12/13/2022]
Abstract
Rhodococci are bacteria which can survive under various extreme conditions, in the presence of toxic compounds, and in other hostile habitats. Their tolerance of unfavorable conditions is associated with the structure of their cell wall and their large array of enzymes, which degrade or detoxify harmful compounds. Their physiological and biotechnological properties, together with tools for their genetic manipulation, enable us to apply them in biotransformations, biodegradation and bioremediation. Many such biotechnological applications cause stresses that positively or negatively affect their efficiency. Whereas numerous reviews on rhodococci described their enzyme activities, the optimization of degradation or production processes, and corresponding technological solutions, only a few reviews discussed some specific effects of stresses on the physiology of rhodococci and biotechnological processes. This review aims to comprehensively describe individual stress responses in Rhodococcus strains, the interconnection of different types of stresses and their consequences for cell physiology. We examine here the responses to (1) environmental stresses (desiccation, heat, cold, osmotic and pH stress), (2) the presence of stress-inducing compounds (metals, organic compounds and antibiotics) in the environment (3) starvation and (4) stresses encountered during biotechnological applications. Adaptations of the cell envelope, the formation of multicellular structures and stresses induced by the interactions of hosts with pathogenic rhodococci are also included. The roles of sigma factors of RNA polymerase in the global regulation of stress responses in rhodococci are described as well. Although the review covers a large number of stressful conditions, our intention was to provide an overview of the selected stress responses and their possible connection to biotechnological processes, not an exhaustive survey of the scientific literature. The findings on stress responses summarized in this review and the demonstration of gaps in current knowledge may motivate researchers working to fill these gaps.
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Affiliation(s)
- Miroslav Pátek
- Institute of Microbiology of the CAS, v. v. i., Prague, Czech Republic.
| | - Michal Grulich
- Institute of Microbiology of the CAS, v. v. i., Prague, Czech Republic.
| | - Jan Nešvera
- Institute of Microbiology of the CAS, v. v. i., Prague, Czech Republic.
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12
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Perczyk P, Wójcik A, Hachlica N, Wydro P, Broniatowski M. The composition of phospholipid model bacterial membranes determines their endurance to secretory phospholipase A2 attack – The role of cardiolipin. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183239. [DOI: 10.1016/j.bbamem.2020.183239] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 02/12/2020] [Accepted: 02/13/2020] [Indexed: 10/24/2022]
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13
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Construction and analysis of an engineered Escherichia coli-Pseudomonas aeruginosa co-culture consortium for phenanthrene bioremoval. Biochem Eng J 2019. [DOI: 10.1016/j.bej.2019.05.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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14
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Oxidative stress under low oxygen conditions triggers hyperflagellation and motility in the Antarctic bacterium Pseudomonas extremaustralis. Extremophiles 2019; 23:587-597. [PMID: 31250111 DOI: 10.1007/s00792-019-01110-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 06/17/2019] [Indexed: 12/14/2022]
Abstract
Reactive oxygen species and nitrogen species (ROS and RNS), produced in a wide range of physiological process even under low oxygen availability, are among the main stressors found in the environment. Strategies developed to combat them constitute key features in bacterial adaptability and survival. Pseudomonas extremaustralis is a metabolic versatile and stress resistant Antarctic bacterium, able to grow under different oxygen conditions. The present work explores the effect of oxidative stress under low oxygen conditions in P. extremaustralis, by combining RNA deep sequencing analysis and physiological studies. Cells grown under microaerobiosis exhibited more oxidative damage in macromolecules and lower survival rates than under aerobiosis. RNA-seq analysis showed an up-regulation of genes related with oxidative stress response, flagella, chemotaxis and biofilm formation while chaperones and cytochromes were down-regulated. Microaerobic cultures exposed to H2O2 also displayed a hyper-flagellated phenotype coupled with a high motility behavior. Moreover, cells that were subjected to oxidative stress presented increased biofilm formation. Altogether, our results suggest that a higher motile behavior and augmented capacity to form biofilm structures could work in addition to well-known antioxidant enzymes and non-enzymatic ROS scavenging mechanisms to cope with oxidative stress at low oxygen tensions.
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15
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Tiwari P, Gosain TP, Singh M, Sankhe GD, Arora G, Kidwai S, Agarwal S, Chugh S, Saini DK, Singh R. Inorganic polyphosphate accumulation suppresses the dormancy response and virulence in Mycobacterium tuberculosis. J Biol Chem 2019; 294:10819-10832. [PMID: 31113860 DOI: 10.1074/jbc.ra119.008370] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 05/07/2019] [Indexed: 11/06/2022] Open
Abstract
Stringent response pathways involving inorganic polyphosphate (PolyP) play an essential role in bacterial stress adaptation and virulence. The intracellular levels of PolyP are modulated by the activities of polyphosphate kinase-1 (PPK1), polyphosphate kinase-2 (PPK2), and exopolyphosphatases (PPXs). The genome of Mycobacterium tuberculosis encodes two functional PPXs, and simultaneous deletion of ppx1 and ppx2 results in a defect in biofilm formation. We demonstrate here that these PPXs cumulatively contribute to the ability of M. tuberculosis to survive in nutrient-limiting, low-oxygen growth conditions and also in macrophages. Characterization of single (Δppx2) and double knockout (dkppx) strains of M. tuberculosis indicated that PPX-mediated PolyP degradation is essential for establishing bacterial infection in guinea pigs. RNA-Seq-based transcriptional profiling revealed that relative to the parental strain, the expression levels of DosR regulon-regulated dormancy genes were significantly reduced in the dkppx mutant strain. In concordance, we also provide evidence that PolyP inhibits the autophosphorylation activities associated with DosT and DosS sensor kinases. The results in this study uncover that enzymes involved in PolyP homeostasis play a critical role in M. tuberculosis physiology and virulence and are attractive targets for developing more effective therapeutic interventions.
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Affiliation(s)
- Prabhakar Tiwari
- Tuberculosis Research Laboratory, Vaccine and Infectious Disease Research Centre, Translational Health Science and Technology Institute, Haryana 121001, India and
| | - Tannu Priya Gosain
- Tuberculosis Research Laboratory, Vaccine and Infectious Disease Research Centre, Translational Health Science and Technology Institute, Haryana 121001, India and
| | - Mamta Singh
- Tuberculosis Research Laboratory, Vaccine and Infectious Disease Research Centre, Translational Health Science and Technology Institute, Haryana 121001, India and
| | | | - Garima Arora
- Tuberculosis Research Laboratory, Vaccine and Infectious Disease Research Centre, Translational Health Science and Technology Institute, Haryana 121001, India and
| | - Saqib Kidwai
- Tuberculosis Research Laboratory, Vaccine and Infectious Disease Research Centre, Translational Health Science and Technology Institute, Haryana 121001, India and
| | - Sakshi Agarwal
- Tuberculosis Research Laboratory, Vaccine and Infectious Disease Research Centre, Translational Health Science and Technology Institute, Haryana 121001, India and
| | - Saurabh Chugh
- Tuberculosis Research Laboratory, Vaccine and Infectious Disease Research Centre, Translational Health Science and Technology Institute, Haryana 121001, India and
| | - Deepak K Saini
- Centre for BioSystems Science and Engineering and; Department of Molecular Reproduction, Development, and Genetics, Biological Sciences Building, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Ramandeep Singh
- Tuberculosis Research Laboratory, Vaccine and Infectious Disease Research Centre, Translational Health Science and Technology Institute, Haryana 121001, India and.
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Suvorova IA, Gelfand MS. Comparative Genomic Analysis of the Regulation of Aromatic Metabolism in Betaproteobacteria. Front Microbiol 2019; 10:642. [PMID: 30984152 PMCID: PMC6449761 DOI: 10.3389/fmicb.2019.00642] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 03/14/2019] [Indexed: 01/23/2023] Open
Abstract
Aromatic compounds are a common carbon and energy source for many microorganisms, some of which can even degrade toxic chloroaromatic xenobiotics. This comparative study of aromatic metabolism in 32 Betaproteobacteria species describes the links between several transcription factors (TFs) that control benzoate (BenR, BenM, BoxR, BzdR), catechol (CatR, CatM, BenM), chlorocatechol (ClcR), methylcatechol (MmlR), 2,4-dichlorophenoxyacetate (TfdR, TfdS), phenol (AphS, AphR, AphT), biphenyl (BphS), and toluene (TbuT) metabolism. We characterize the complexity and variability in the organization of aromatic metabolism operons and the structure of regulatory networks that may differ even between closely related species. Generally, the upper parts of pathways, rare pathway variants, and degradative pathways of exotic and complex, in particular, xenobiotic compounds are often controlled by a single TF, while the regulation of more common and/or central parts of the aromatic metabolism may vary widely and often involves several TFs with shared and/or dual, or cascade regulation. The most frequent and at the same time variable connections exist between AphS, AphR, AphT, and BenR. We have identified a novel LysR-family TF that regulates the metabolism of catechol (or some catechol derivative) and either substitutes CatR(M)/BenM, or shares functions with it. We have also predicted several new members of aromatic metabolism regulons, in particular, some COGs regulated by several different TFs.
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Affiliation(s)
- Inna A Suvorova
- Institute for Information Transmission Problems RAS (The Kharkevich Institute), Moscow, Russia
| | - Mikhail S Gelfand
- Institute for Information Transmission Problems RAS (The Kharkevich Institute), Moscow, Russia.,Faculty of Computer Science, Higher School of Economics, Moscow, Russia.,Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
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Sulfurimonas subgroup GD17 cells accumulate polyphosphate under fluctuating redox conditions in the Baltic Sea: possible implications for their ecology. ISME JOURNAL 2018; 13:482-493. [PMID: 30291329 DOI: 10.1038/s41396-018-0267-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 05/04/2018] [Accepted: 05/11/2018] [Indexed: 12/16/2022]
Abstract
The central Baltic Sea is characterized by a pelagic redox zone exhibiting high dark CO2 fixation rates below the chemocline. These rates are mainly driven by chemolithoautotrophic and denitrifying Sulfurimonas GD17 subgroup cells which are motile and fast-reacting r-strategists. Baltic Sea redox zones are unstable and a measurable overlap of nitrate and reduced sulfur, essential for chemosynthesis, is often only available on small scales and short times due to local mixing events. This raises the question of how GD17 cells gain access to electron donors or acceptors over longer term periods and under substrate deficiency. One possible answer is that GD17 cells store high-energy-containing polyphosphate during favorable nutrient conditions to survive periods of nutrient starvation. We used scanning electron microscopy with energy-dispersive X-ray spectroscopy to investigate potential substrate enrichments in single GD17 cells collected from Baltic Sea redox zones. More specific substrate enrichment features were identified in experiments using Sulfurimonas gotlandica GD1T, a GD17 representative. Sulfurimonas cells accumulated polyphosphate both in situ and in vitro. Combined genome and culture-dependent analyses suggest that polyphosphate serves as an energy reservoir to maintain cellular integrity at unfavorable substrate conditions. This redox-independent energy supply would be a precondition for sustaining the r-strategy lifestyle of GD17 and may represent a newly identified survival strategy for chemolithoautotrophic prokaryotes occupying eutrophic redox zones.
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18
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Akkaya Ö, Pérez-Pantoja DR, Calles B, Nikel PI, de Lorenzo V. The Metabolic Redox Regime of Pseudomonas putida Tunes Its Evolvability toward Novel Xenobiotic Substrates. mBio 2018; 9:e01512-18. [PMID: 30154264 PMCID: PMC6113623 DOI: 10.1128/mbio.01512-18] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 07/23/2018] [Indexed: 12/28/2022] Open
Abstract
During evolution of biodegradation pathways for xenobiotic compounds involving Rieske nonheme iron oxygenases, the transition toward novel substrates is frequently associated with faulty reactions. Such events release reactive oxygen species (ROS), which are endowed with high mutagenic potential. In this study, we evaluated how the operation of the background metabolic network by an environmental bacterium may either foster or curtail the still-evolving pathway for 2,4-dinitrotoluene (2,4-DNT) catabolism. To this end, the genetically tractable strain Pseudomonas putida EM173 was implanted with the whole genetic complement necessary for the complete biodegradation of 2,4-DNT (recruited from the environmental isolate Burkholderia sp. R34). By using reporter technology and direct measurements of ROS formation, we observed that the engineered P. putida strain experienced oxidative stress when catabolizing the nitroaromatic substrate. However, the formation of ROS was neither translated into significant activation of the SOS response to DNA damage nor did it result in a mutagenic regime (unlike what has been observed in Burkholderia sp. R34, the original host of the pathway). To inspect whether the tolerance of P. putida to oxidative challenges could be traced to its characteristic reductive redox regime, we artificially altered the NAD(P)H pool by means of a water-forming, NADH-specific oxidase. Under the resulting low-NAD(P)H status, catabolism of 2,4-DNT triggered a conspicuous mutagenic and genomic diversification scenario. These results indicate that the background biochemical network of environmental bacteria ultimately determines the evolvability of metabolic pathways. Moreover, the data explain the efficacy of some bacteria (e.g., pseudomonads) to host and evolve with new catabolic routes.IMPORTANCE Some environmental bacteria evolve with new capacities for the aerobic biodegradation of chemical pollutants by adapting preexisting redox reactions to novel compounds. The process typically starts by cooption of enzymes from an available route to act on the chemical structure of the substrate-to-be. The critical bottleneck is generally the first biochemical step, and most of the selective pressure operates on reshaping the initial reaction. The interim uncoupling of the novel substrate to preexisting Rieske nonheme iron oxygenases usually results in formation of highly mutagenic ROS. In this work, we demonstrate that the background metabolic regime of the bacterium that hosts an evolving catabolic pathway (e.g., biodegradation of the xenobiotic 2,4-DNT) determines whether the cells either adopt a genetic diversification regime or a robust ROS-tolerant status. Furthermore, our results offer new perspectives to the rational design of efficient whole-cell biocatalysts, which are pursued in contemporary metabolic engineering.
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Affiliation(s)
- Özlem Akkaya
- Department of Molecular Biology and Genetics, Faculty of Sciences, Gebze Technical University, Kocaeli, Turkey
| | - Danilo R Pérez-Pantoja
- Programa Institucional de Fomento a la Investigación, Desarrollo e Innovación, Universidad Tecnológica Metropolitana, Santiago de Chile, Chile
| | - Belén Calles
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología, Madrid, Spain
| | - Pablo I Nikel
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Víctor de Lorenzo
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología, Madrid, Spain
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19
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Murugan K, Vasudevan N. Intracellular toxicity exerted by PCBs and role of VBNC bacterial strains in biodegradation. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2018; 157:40-60. [PMID: 29605643 DOI: 10.1016/j.ecoenv.2018.03.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 02/22/2018] [Accepted: 03/06/2018] [Indexed: 06/08/2023]
Abstract
Polychlorinated biphenyls (PCBs) are xenobiotic compounds that persists in the environment for long-term, though its productivity is banned. Abatement of the pollutants have become laborious due to it's recalcitrant nature in the environment leading to toxic effects in humans and other living beings. Biphenyl degrading bacteria co-metabolically degrade low chlorinated PCBs using the active metabolic pathway. bph operon possess different genetic arrangements in gram positive and gram negative bacteria. The binding ability of the genes and the active sites were determined by PCB docking studies. The active site of bphA gene with conserved amino acid residues determines the substrate specificity and biodegradability. Accumulation of toxic intermediates alters cellular behaviour, biomass production and downturn the metabolic activity. Several bacteria in the environment attain unculturable state which is viable and metabolically active but not cultivable (VBNC). Resuscitation-promoting factor (Rpf) and Rpf homologous protein retrieve the culturability of the so far uncultured bacteria. Recovery of this adaptive mechanism against various physical and chemical stressors make a headway in understanding the functionality of both environmental and medically important unculturable bacteria. Thus, this paper review about the general aspects of PCBs, cellular toxicity exerted by PCBs, role of unculturable bacterial strains in biodegradation, genes involved and degradation pathways. It is suggested to extrapolate the research findings on extracellular organic matters produced in culture supernatant of VBNC thus transforming VBNC to culturable state.
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Affiliation(s)
- Karuvelan Murugan
- Centre for Environmental Studies, Anna University, CEG Campus, Chennai, Tamil Nadu, India.
| | - Namasivayam Vasudevan
- Centre for Environmental Studies, Anna University, CEG Campus, Chennai, Tamil Nadu, India.
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20
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Sazykin IS, Sazykina MA, Khmelevtsova LE, Seliverstova EY, Karchava KS, Zhuravleva MV. Antioxidant enzymes and reactive oxygen species level of the Achromobacter xylosoxidans bacteria during hydrocarbons biotransformation. Arch Microbiol 2018; 200:1057-1065. [PMID: 29687314 DOI: 10.1007/s00203-018-1516-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 12/18/2017] [Accepted: 04/05/2018] [Indexed: 11/28/2022]
Abstract
The level of catalase and superoxide dismutase induction, as well as generation of superoxide anion radical in cells and accumulation of hydrogen peroxide in the culture medium were researched in three strains of oil-degrading bacteria Achromobacter xylosoxidans at cultivation in rich nutrient medium and in the media with hydrocarbons as the only source of carbon. The effects of pentane, decane, hexadecane, cyclohexane, benzene, naphthalene and diesel fuel were evaluated. It was determined that in the microbial cell on media with hydrocarbons, the generation of superoxide anion radical increases, accumulation of hydrogen peroxide and induction of superoxide dismutase synthesis occur, and catalase activity is reduced. Oxidative stress in the cells of A. xylosoxidans was caused by biotransformation of all the studied hydrocarbons. The most pronounced effect was observed at incubation of bacteria with cyclohexane, pentane, diesel fuel, benzene and naphthalene.
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Affiliation(s)
- I S Sazykin
- Southern Federal University, Stachki, 194/1, Rostov-on-Don, 344090, Russia
| | - M A Sazykina
- Southern Federal University, Stachki, 194/1, Rostov-on-Don, 344090, Russia.
| | - L E Khmelevtsova
- Southern Federal University, Stachki, 194/1, Rostov-on-Don, 344090, Russia
| | - E Yu Seliverstova
- Southern Federal University, Stachki, 194/1, Rostov-on-Don, 344090, Russia
| | - K Sh Karchava
- Southern Federal University, Stachki, 194/1, Rostov-on-Don, 344090, Russia
| | - M V Zhuravleva
- Southern Federal University, Stachki, 194/1, Rostov-on-Don, 344090, Russia
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21
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Inorganic polyphosphate in methylotrophic yeasts. Appl Microbiol Biotechnol 2018; 102:5235-5244. [DOI: 10.1007/s00253-018-9008-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 04/05/2018] [Accepted: 04/07/2018] [Indexed: 12/23/2022]
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22
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Presentato A, Cappelletti M, Sansone A, Ferreri C, Piacenza E, Demeter MA, Crognale S, Petruccioli M, Milazzo G, Fedi S, Steinbüchel A, Turner RJ, Zannoni D. Aerobic Growth of Rhodococcus aetherivorans BCP1 Using Selected Naphthenic Acids as the Sole Carbon and Energy Sources. Front Microbiol 2018; 9:672. [PMID: 29706937 PMCID: PMC5906575 DOI: 10.3389/fmicb.2018.00672] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 03/22/2018] [Indexed: 11/13/2022] Open
Abstract
Naphthenic acids (NAs) are an important group of toxic organic compounds naturally occurring in hydrocarbon deposits. This work shows that Rhodococcus aetherivorans BCP1 cells not only utilize a mixture of eight different NAs (8XNAs) for growth but they are also capable of marked degradation of two model NAs, cyclohexanecarboxylic acid (CHCA) and cyclopentanecarboxylic acid (CPCA) when supplied at concentrations from 50 to 500 mgL-1. The growth curves of BCP1 on 8XNAs, CHCA, and CPCA showed an initial lag phase not present in growth on glucose, which presumably was related to the toxic effects of NAs on the cell membrane permeability. BCP1 cell adaptation responses that allowed survival on NAs included changes in cell morphology, production of intracellular bodies and changes in fatty acid composition. Transmission electron microscopy (TEM) analysis of BCP1 cells grown on CHCA or CPCA showed a slight reduction in the cell size, the production of EPS-like material and intracellular electron-transparent and electron-dense inclusion bodies. The electron-transparent inclusions increased in the amount and size in NA-grown BCP1 cells under nitrogen limiting conditions and contained storage lipids as suggested by cell staining with the lipophilic Nile Blue A dye. Lipidomic analyses revealed significant changes with increases of methyl-branched (MBFA) and polyunsaturated fatty acids (PUFA) examining the fatty acid composition of NAs-growing BCP1 cells. PUFA biosynthesis is not usual in bacteria and, together with MBFA, can influence structural and functional processes with resulting effects on cell vitality. Finally, through the use of RT (Reverse Transcription)-qPCR, a gene cluster (chcpca) was found to be transcriptionally induced during the growth on CHCA and CPCA. Based on the expression and bioinformatics results, the predicted products of the chcpca gene cluster are proposed to be involved in aerobic NA degradation in R. aetherivorans BCP1. This study provides first insights into the genetic and metabolic mechanisms allowing a Rhodococcus strain to aerobically degrade NAs.
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Affiliation(s)
- Alessandro Presentato
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Martina Cappelletti
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Anna Sansone
- ISOF, Consiglio Nazionale delle Ricerche, Bologna, Italy
| | - Carla Ferreri
- ISOF, Consiglio Nazionale delle Ricerche, Bologna, Italy
| | - Elena Piacenza
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Marc A. Demeter
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Silvia Crognale
- Department for Innovation in Biological, Agro-food and Forest Systems (DIBAF), University of Tuscia, Viterbo, Italy
| | - Maurizio Petruccioli
- Department for Innovation in Biological, Agro-food and Forest Systems (DIBAF), University of Tuscia, Viterbo, Italy
| | - Giorgio Milazzo
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Stefano Fedi
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Alexander Steinbüchel
- Institute of Molecular Microbiology and Biotechnology, University of Münster, Münster, Germany
- Department of Environmental Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Raymond J. Turner
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Davide Zannoni
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
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23
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Sandri F, Musiani F, Selamoglu N, Daldal F, Zannoni D. Pseudomonas pseudoalcaligenes KF707 grown with biphenyl expresses a cytochrome caa 3 oxidase that uses cytochrome c 4 as electron donor. FEBS Lett 2018; 592:901-915. [PMID: 29427514 DOI: 10.1002/1873-3468.13001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 01/30/2018] [Accepted: 02/01/2018] [Indexed: 11/09/2022]
Abstract
Combining peroxidase activity-based heme staining (TMBZ/SDS/PAGE) with mass spectrometry analyses (Nano LC-MS/MS) of protein extracts from wild-type and appropriate mutants, we provide evidence that the polychlorinated biphenyl degrader Pseudomonas pseudoalcaligenes KF707 primarily expresses a caa3 -type cytochrome c oxidase (caa3 -Cox) using cytochrome (cyt) c4 as an electron donor in cells grown with biphenyl versus glucose as the sole carbon source. Homology modeling of KF707 caa3 -Cox using the three-dimensional structure of that from Thermus thermophilus highlights multiple similarities and differences between the proton channels in subunit I of the aa3 - and caa3 -Cox of Paracoccus and Thermus spp., respectively. To our knowledge, this is the first report demonstrating the presence of a caa3 -Cox using cyt c4 as an electron donor in a Pseudomonas species.
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Affiliation(s)
- Federica Sandri
- Department of Pharmacy and BioTechnology, University of Bologna, Italy
| | - Francesco Musiani
- Department of Pharmacy and BioTechnology, University of Bologna, Italy
| | - Nur Selamoglu
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Fevzi Daldal
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Davide Zannoni
- Department of Pharmacy and BioTechnology, University of Bologna, Italy
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Lemire J, Alhasawi A, Appanna VP, Tharmalingam S, Appanna VD. Metabolic defence against oxidative stress: the road less travelled so far. J Appl Microbiol 2017; 123:798-809. [PMID: 28609580 DOI: 10.1111/jam.13509] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 05/30/2017] [Accepted: 06/05/2017] [Indexed: 12/28/2022]
Abstract
Bacteria have survived, and many have thrived, since antiquity in the presence of the highly-reactive chalcogen-oxygen (O2 ). They are known to evoke intricate strategies to defend themselves from the reactive by-products of oxygen-reactive oxygen species (ROS). Many of these detoxifying mechanisms have been extensively characterized; superoxide dismutase, catalases, alkyl hydroperoxide reductase and the glutathione (GSH)-cycling system are responsible for neutralizing specific ROS. Meanwhile, a pool of NADPH-the reductive engine of many ROS-combating enzymes-is maintained by metabolic enzymes including, but not exclusively, glucose-6 phosphate dehydrogenase (G6PDH) and NADP-dependent isocitrate dehydrogenase (ICDH-NADP). So, it is not surprising that evidence continues to emerge demonstrating the pivotal role metabolism plays in mitigating ROS toxicity. Stemming from its ability to concurrently decrease the production of the pro-oxidative metabolite, NADH, while augmenting the antioxidative metabolite, NADPH, metabolism is the fulcrum of cellular redox potential. In this review, we will discuss the mounting evidence positioning metabolism and metabolic shifts observed during oxidative stress, as critical strategies microbes utilize to thrive in environments that are rife with ROS. The contribution of ketoacids-moieties capable of non-enzymatic decarboxylation in the presence of oxidants-as ROS scavengers will be elaborated alongside the metabolic pathways responsible for their homeostases. Further, the signalling role of the carboxylic acids generated following the ketoacid-mediated detoxification of the ROS will be commented on within the context of oxidative stress.
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Affiliation(s)
- J Lemire
- The Biofilm Research Group, The Department of Biological Sciences, The University of Calgary, Calgary, AB, Canada
| | - A Alhasawi
- Faculty of Science & Engineering, Laurentian University, Sudbury, ON, Canada
| | - V P Appanna
- Faculty of Science & Engineering, Laurentian University, Sudbury, ON, Canada
| | - S Tharmalingam
- Faculty of Science & Engineering, Laurentian University, Sudbury, ON, Canada
| | - V D Appanna
- Faculty of Science & Engineering, Laurentian University, Sudbury, ON, Canada
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25
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Agulló L, Romero-Silva MJ, Domenech M, Seeger M. p-Cymene Promotes Its Catabolism through the p-Cymene and the p-Cumate Pathways, Activates a Stress Response and Reduces the Biofilm Formation in Burkholderia xenovorans LB400. PLoS One 2017; 12:e0169544. [PMID: 28072820 PMCID: PMC5224996 DOI: 10.1371/journal.pone.0169544] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 12/18/2016] [Indexed: 11/19/2022] Open
Abstract
p-Cymene is an aromatic terpene that is present in diverse plant species. The aims of this study were to study the p-cymene metabolism in the model aromatic-degrading bacterium Burkholderia xenovorans LB400, and its response to p-cymene. The catabolic p-cymene (cym) and p-cumate (cmt) genes are clustered on the LB400 major chromosome. B. xenovorans LB400 was able to grow on p-cymene as well as on p-cumate as a sole carbon and energy sources. LB400 growth attained higher cell concentration at stationary phase on p-cumate than on p-cymene. The transcription of the key cymAb and cmtAb genes, and p-cumate dioxygenase activity were observed in LB400 cells grown on p-cymene and on p-cumate, but not in glucose-grown cells. Diverse changes on LB400 proteome were observed in p-cymene-grown cells compared to glucose-grown cells. An increase of the molecular chaperones DnaK, GroEL and ClpB, the organic hydroperoxide resistance protein Ohr, the alkyl hydroperoxide reductase AhpC and the copper oxidase CopA during growth on p-cymene strongly suggests that the exposure to p-cymene constitutes a stress condition for strain LB400. Diverse proteins of the energy metabolism such as enolase, pyruvate kinase, aconitase AcnA, succinyl-CoA synthetase beta subunit and ATP synthase beta subunit were induced by p-cymene. Electron microscopy showed that p-cymene-grown cells exhibited fuzzy outer and inner membranes and an increased periplasm. p-Cymene induced diverse membrane and transport proteins including the p-cymene transporter CymD. Biofilm formation was reduced during growth in p-cymene in strain LB400 compared to glucose-grown cells that may be associated with a decrease of diguanylate cyclase protein levels. Overall, these results indicate active p-cymene and p-cumate catabolic pathways in B. xenovorans LB400. In addition, this study showed that p-cymene activated a stress response in strain LB400 and reduced its biofilm formation.
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Affiliation(s)
- Loreine Agulló
- Molecular Microbiology and Environmental Biotechnology Laboratory, Department of Chemistry & Center for Nanotechnology and Systems Biology, Centro de Biotecnología, Universidad Técnica Federico Santa María, Valparaíso, Chile
| | - María José Romero-Silva
- Molecular Microbiology and Environmental Biotechnology Laboratory, Department of Chemistry & Center for Nanotechnology and Systems Biology, Centro de Biotecnología, Universidad Técnica Federico Santa María, Valparaíso, Chile
| | - Mirian Domenech
- Departamento de Microbiología Molecular y Biología de las Infecciones, Centro de Investigaciones Biológicas (CSIC), Madrid, Spain
| | - Michael Seeger
- Molecular Microbiology and Environmental Biotechnology Laboratory, Department of Chemistry & Center for Nanotechnology and Systems Biology, Centro de Biotecnología, Universidad Técnica Federico Santa María, Valparaíso, Chile
- * E-mail:
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26
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Varas M, Valdivieso C, Mauriaca C, Ortíz-Severín J, Paradela A, Poblete-Castro I, Cabrera R, Chávez FP. Multi-level evaluation of Escherichia coli polyphosphate related mutants using global transcriptomic, proteomic and phenomic analyses. Biochim Biophys Acta Gen Subj 2017; 1861:871-883. [PMID: 28069396 DOI: 10.1016/j.bbagen.2017.01.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 12/26/2016] [Accepted: 01/05/2017] [Indexed: 12/20/2022]
Abstract
BACKGROUND Polyphosphate (polyP) is a linear biopolymer found in all living cells. In bacteria, mutants lacking polyphosphate kinase 1 (PPK1), the enzyme responsible for synthesis of most polyP, have many structural and functional defects. However, little is known about the causes of these pleiotropic alterations. The link between ppk1 deletion and those numerous phenotypes observed can be the result of complex molecular interactions that can be elucidated via a systems biology approach. METHODS By integrating different omics levels (transcriptome, proteome and phenome), we described the functioning of various metabolic pathways among Escherichia coli polyphosphate mutant strains (Δppk1, Δppx, and ΔpolyP). Bioinformatic analyses reveal the complex metabolic and regulatory bases of the phenotypes unique to polyP mutants. RESULTS Our results suggest that during polyP deficiency (Δppk1 mutant), metabolic pathways needed for energy supply are up-regulated, including fermentation, aerobic and anaerobic respiration. Transcriptomic and q-proteomic contrasting changes between Δppk1 and Δppx mutant strains were observed in those central metabolic pathways and confirmed by using Phenotypic microarrays. In addition, our results suggest a regulatory connection between polyP, second messenger metabolism, alternative Sigma/Anti-Sigma factors and type-II toxin-antitoxin (TA) systems. CONCLUSIONS We suggest a broader role for polyP via regulation of ATP-dependent proteolysis of type II toxin-antitoxin system and alternative Sigma/Anti-Sigma factors, that could explain the multiple structural and functional deficiencies described due to alteration of polyP metabolism. GENERAL SIGNIFICANCE Understanding the interplay of polyP in bacterial metabolism using a systems biology approach can help to improve design of novel antimicrobials toward pathogens.
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Affiliation(s)
- Macarena Varas
- Systems Microbiology Laboratory, Department of Biology, Faculty of Science, University of Chile, Chile.
| | - Camilo Valdivieso
- Systems Microbiology Laboratory, Department of Biology, Faculty of Science, University of Chile, Chile; Department of Ecology, Faculty of Science, University of Chile, Chile.
| | - Cecilia Mauriaca
- Systems Microbiology Laboratory, Department of Biology, Faculty of Science, University of Chile, Chile.
| | - Javiera Ortíz-Severín
- Systems Microbiology Laboratory, Department of Biology, Faculty of Science, University of Chile, Chile.
| | | | - Ignacio Poblete-Castro
- Facultad de Ciencias Biológicas, Center for Bioinformatics and Integrative Biology, Biosystems Engineering Laboratory, Universidad Andrés Bello, Chile.
| | - Ricardo Cabrera
- Department of Biology, Faculty of Sciences, University of Chile, Chile.
| | - Francisco P Chávez
- Systems Microbiology Laboratory, Department of Biology, Faculty of Science, University of Chile, Chile.
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27
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Chakraborty J, Das S. Molecular perspectives and recent advances in microbial remediation of persistent organic pollutants. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:16883-16903. [PMID: 27234838 DOI: 10.1007/s11356-016-6887-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 05/11/2016] [Indexed: 06/05/2023]
Abstract
Nutrition and pollution stress stimulate genetic adaptation in microorganisms and assist in evolution of diverse metabolic pathways for their survival on several complex organic compounds. Persistent organic pollutants (POPs) are highly lipophilic in nature and cause adverse effects to the environment and human health by biomagnification through the food chain. Diverse microorganisms, harboring numerous plasmids and catabolic genes, acclimatize to these environmentally unfavorable conditions by gene duplication, mutational drift, hypermutation, and recombination. Genetic aspects of some major POP catabolic genes such as biphenyl dioxygenase (bph), DDT 2,3-dioxygenase, and angular dioxygenase assist in degradation of biphenyl, organochlorine pesticides, and dioxins/furans, respectively. Microbial metagenome constitutes the largest genetic reservoir with miscellaneous enzymatic activities implicated in degradation. To tap the metabolic potential of microorganisms, recent techniques like sequence and function-based screening and substrate-induced gene expression are proficient in tracing out novel catabolic genes from the entire metagenome for utilization in enhanced biodegradation. The major endeavor of today's scientific world is to characterize the exact genetic mechanisms of microbes for bioremediation of these toxic compounds by excavating into the uncultured plethora. This review entails the effect of POPs on the environment and involvement of microbial catabolic genes for their removal with the advanced techniques of bioremediation.
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Affiliation(s)
- Jaya Chakraborty
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, 769 008, Odisha, India
| | - Surajit Das
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, 769 008, Odisha, India.
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Booth SC, Weljie AM, Turner RJ. Metabolomics reveals differences of metal toxicity in cultures of Pseudomonas pseudoalcaligenes KF707 grown on different carbon sources. Front Microbiol 2015; 6:827. [PMID: 26347721 PMCID: PMC4538868 DOI: 10.3389/fmicb.2015.00827] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 07/27/2015] [Indexed: 12/23/2022] Open
Abstract
Co-contamination of metals and organic pollutants is a global problem as metals interfere with the metabolism of complex organics by bacteria. Based on a prior observation that metal tolerance was altered by the sole carbon source being used for growth, we sought to understand how metal toxicity specifically affects bacteria using an organic pollutant as their sole carbon source. To this end metabolomics was used to compare cultures of Pseudomonas pseudoalcaligenes KF707 grown on either biphenyl (Bp) or succinate (Sc) as the sole carbon source in the presence of either aluminum (Al) or copper (Cu). Using multivariate statistical analysis it was found that the metals caused perturbations to more cellular processes in the cultures grown on Bp than those grown on Sc. Al induced many changes that were indicative of increased oxidative stress as metabolites involved in DNA damage and protection, the Krebs cycle and anti-oxidant production were altered. Cu also caused metabolic changes that were indicative of similar stress, as well as appearing to disrupt other key enzymes such as fumarase. Additionally, both metals caused the accumulation of Bp degradation intermediates indicating that they interfered with Bp metabolism. Together these results provide a basic understanding of how metal toxicity specifically affects bacteria at a biochemical level during the degradation of an organic pollutant and implicate the catabolism of this carbon source as a major factor that exacerbates metal toxicity.
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Affiliation(s)
- Sean C Booth
- Department of Biological Sciences, University of Calgary, Calgary AB, Canada
| | - Aalim M Weljie
- Department of Biological Sciences, University of Calgary, Calgary AB, Canada ; Department of Systems Pharmacology and Translational Therapeutics, Smilow Centre for Translational Research, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA, USA
| | - Raymond J Turner
- Department of Biological Sciences, University of Calgary, Calgary AB, Canada ; Biofilm Research Group, University of Calgary, Calgary AB, Canada
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29
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The Confluence of Heavy Metal Biooxidation and Heavy Metal Resistance: Implications for Bioleaching by Extreme Thermoacidophiles. MINERALS 2015. [DOI: 10.3390/min5030397] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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30
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Bhat SV, Booth SC, McGrath SGK, Dahms TES. Rhizobium leguminosarum bv. viciae 3841 Adapts to 2,4-Dichlorophenoxyacetic Acid with "Auxin-Like" Morphological Changes, Cell Envelope Remodeling and Upregulation of Central Metabolic Pathways. PLoS One 2015; 10:e0123813. [PMID: 25919284 PMCID: PMC4412571 DOI: 10.1371/journal.pone.0123813] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 03/07/2015] [Indexed: 11/18/2022] Open
Abstract
There is a growing need to characterize the effects of environmental stressors at the molecular level on model organisms with the ever increasing number and variety of anthropogenic chemical pollutants. The herbicide 2,4-dichlorophenoxyacetic acid (2,4-D), as one of the most widely applied pesticides in the world, is one such example. This herbicide is known to have non-targeted undesirable effects on humans, animals and soil microbes, but specific molecular targets at sublethal levels are unknown. In this study, we have used Rhizobium leguminosarum bv. viciae 3841 (Rlv) as a nitrogen fixing, beneficial model soil organism to characterize the effects of 2,4-D. Using metabolomics and advanced microscopy we determined specific target pathways in the Rlv metabolic network and consequent changes to its phenotype, surface ultrastructure, and physical properties during sublethal 2,4-D exposure. Auxin and 2,4-D, its structural analogue, showed common morphological changes in vitro which were similar to bacteroids isolated from plant nodules, implying that these changes are related to bacteroid differentiation required for nitrogen fixation. Rlv showed remarkable adaptation capabilities in response to the herbicide, with changes to integral pathways of cellular metabolism and the potential to assimilate 2,4-D with consequent changes to its physical and structural properties. This study identifies biomarkers of 2,4-D in Rlv and offers valuable insights into the mode-of-action of 2,4-D in soil bacteria.
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Affiliation(s)
- Supriya V. Bhat
- Department of Chemistry and Biochemistry, University of Regina, 3737 Wascana Parkway, Regina, SK, S4S 0A2 Canada
| | - Sean C. Booth
- Department of Biological Sciences, University of Calgary, 2500 University Dr, NW Calgary, AB, T2N 1N4 Canada
| | - Seamus G. K. McGrath
- Department of Chemistry and Biochemistry, University of Regina, 3737 Wascana Parkway, Regina, SK, S4S 0A2 Canada
| | - Tanya E. S. Dahms
- Department of Chemistry and Biochemistry, University of Regina, 3737 Wascana Parkway, Regina, SK, S4S 0A2 Canada
- * E-mail:
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31
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Puntus IF, Ryazanova LP, Zvonarev AN, Funtikova TV, Kulakovskaya TV. The role of mineral phosphorus compounds in naphthalene biodegradation by Pseudomonas putida. APPL BIOCHEM MICRO+ 2015. [DOI: 10.1134/s0003683815020143] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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32
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Bourguignon N, Isaac P, Alvarez H, Amoroso MJ, Ferrero MA. Enhanced polyaromatic hydrocarbon degradation by adapted cultures of actinomycete strains. J Basic Microbiol 2014; 54:1288-94. [PMID: 25205070 DOI: 10.1002/jobm.201400262] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 07/05/2014] [Indexed: 11/07/2022]
Abstract
Fifteen actinomycete strains were evaluated for their potential use in removal of polycyclic aromatic hydrocarbons (PAH). Their capability to degrade of naphthalene, phenanthrene, and pyrene was tested in minimal medium (MM) and MM with glucose as another substrate. Degradation of naphthalene in MM was observed in all isolates at different rates, reaching maximum values near to 76% in some strains of Streptomyces, Rhodococcus sp. 016 and Amycolatopsis tucumanensis DSM 45259. Maximum values of degradation of phenanthrene in MM occurred in cultures of A. tucumanensis DSM 45259 (36.2%) and Streptomyces sp. A12 (20%), while the degradation of pyrene in MM was poor and only significant with Streptomyces sp. A12 (4.3%). Because of the poor performance when growing on phenanthrene and pyrene alone, Rhodococcus sp. 20, Rhodococcus sp. 016, A. tucumanensis DSM 45259, Streptomyces sp. A2, and Streptomyces sp. A12 were challenged to an adaptation schedule of successive cultures on a fresh solid medium supplemented with PAHs, decreasing concentration of glucose in each step. As a result, an enhanced degradation of PAHs by adapted strains was observed in the presence of glucose as co-substrate, without degradation of phenanthrene and pyrene in MM while an increase to up to 50% of degradation was seen with these strains in glucose amended media. An internal fragment of the catA gene, which codes for catechol 1,2-dioxygenase, was amplified from both Rhodococcus strains, showing the potential for degradation of aromatic compounds via salycilate. These results allow us to propose the usefulness of these actinomycete strains for PAH bioremediation in the environment.
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Affiliation(s)
- Natalia Bourguignon
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), Tucumán, Argentina
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Giebel HA, Kalhoefer D, Gahl-Janssen R, Choo YJ, Lee K, Cho JC, Tindall BJ, Rhiel E, Beardsley C, Aydogmus ÖO, Voget S, Daniel R, Simon M, Brinkhoff T. Planktomarina temperata gen. nov., sp. nov., belonging to the globally distributed RCA cluster of the marine Roseobacter clade, isolated from the German Wadden Sea. Int J Syst Evol Microbiol 2013; 63:4207-4217. [DOI: 10.1099/ijs.0.053249-0] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Four heterotrophic bacterial strains belonging to the globally distributed marine RCA (Roseobacter clade-affiliated) cluster (family
Rhodobacteraceae
, class
Alphaproteobacteria
) were obtained from coastal seawater samples. Strain RCA23T was isolated from a 10−7 dilution culture inoculated with seawater from the German Wadden Sea (southern North Sea), reflecting the high abundance of RCA bacteria in this habitat. Strains IMCC1909, IMCC1923 and IMCC1933 were isolated from diluted seawater (10−3) of the Yellow Sea, South Korea. Based on 16S rRNA gene sequence comparison,
Octadecabacter antarcticus
307T is the closest described relative of the RCA strains, with 95.4–95.5 % sequence similarity. Cells of RCA23T, IMCC1909, IMCC1923 and IMCC1933 are small motile rods requiring sodium ions. Optimal growth of RCA23T occurs at 25 °C and within a very narrow pH range (pH 7–8, optimum pH 7.5). The DNA G+C base content of RCA23T is 53.67 mol%. The major respiratory lipoquinone is ubiquinone-10 (Q-10) and the dominant fatty acids (>1 %) are 12 : 1 3-OH, 16 : 1ω7c, 16 : 0, 18 : 1ω7c, 18 : 0 and 11-methyl 18 : 1ω7c. The polar lipid pattern indicated the presence of phosphatidylglycerol, two unidentified aminolipids and two unidentified phospholipids. On marine agar, RCA23T forms non-pigmented, transparent to light beige, small (<1 mm), circular, convex colonies. Strain RCA23T harbours all genes for the production of bacteriochlorophyll a (BChl a). Genes encoding the light-harvesting reaction centre of BChl a (pufM) were identified in all RCA strains. No visible pigmentation was observed for any of the strains under laboratory conditions, but spectrophotometric analysis revealed weak production of BChl a by RCA23T. Morphological, physiological and genotypic features of strain RCA23T suggest that it represents a novel species of a new genus within the
Rhodobacteraceae
, for which we propose the name Planktomarina temperata gen. nov., sp. nov., described previously by Giebel et al. [ISME J
5 (2011), 8–19] as ‘Candidatus Planktomarina temperata’. The type strain of Planktomarina temperata is RCA23T ( = DSM 22400T = JCM 18269T).
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Affiliation(s)
- Helge-Ansgar Giebel
- Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, D-26111 Oldenburg, Germany
| | - Daniela Kalhoefer
- Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, D-26111 Oldenburg, Germany
| | - Renate Gahl-Janssen
- Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, D-26111 Oldenburg, Germany
| | - Yoe-Jin Choo
- Division of Biology and Ocean Sciences, Inha University, Incheon, Republic of Korea
| | - Kiyoung Lee
- Division of Biology and Ocean Sciences, Inha University, Incheon, Republic of Korea
| | - Jang-Cheon Cho
- Division of Biology and Ocean Sciences, Inha University, Incheon, Republic of Korea
| | - Brian J. Tindall
- Leibniz Institut DSMZ – Deutsche Sammlung von Mikroorganismen und Zellkulturen, D-38124 Braunschweig, Germany
| | - Erhard Rhiel
- Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, D-26111 Oldenburg, Germany
| | - Christine Beardsley
- Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, D-26111 Oldenburg, Germany
| | - Ömer O. Aydogmus
- Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, D-26111 Oldenburg, Germany
| | - Sonja Voget
- Institute of Microbiology & Genetics, Genomic & Applied Microbiology and Göttingen Genomics Laboratory, University of Göttingen, D-37077 Göttingen, Germany
| | - Rolf Daniel
- Institute of Microbiology & Genetics, Genomic & Applied Microbiology and Göttingen Genomics Laboratory, University of Göttingen, D-37077 Göttingen, Germany
| | - Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, D-26111 Oldenburg, Germany
| | - Thorsten Brinkhoff
- Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, D-26111 Oldenburg, Germany
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Pérez-Pantoja D, Nikel PI, Chavarría M, de Lorenzo V. Endogenous stress caused by faulty oxidation reactions fosters evolution of 2,4-dinitrotoluene-degrading bacteria. PLoS Genet 2013; 9:e1003764. [PMID: 24009532 PMCID: PMC3757077 DOI: 10.1371/journal.pgen.1003764] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Accepted: 07/16/2013] [Indexed: 01/13/2023] Open
Abstract
Environmental strain Burkholderia sp. DNT mineralizes the xenobiotic compound 2,4-dinitrotoluene (DNT) owing to the catabolic dnt genes borne by plasmid DNT, but the process fails to promote significant growth. To investigate this lack of physiological return of such an otherwise complete metabolic route, cells were exposed to DNT under various growth conditions and the endogenous formation of reactive oxygen species (ROS) monitored in single bacteria. These tests revealed the buildup of a strong oxidative stress in the population exposed to DNT. By either curing the DNT plasmid or by overproducing the second activity of the biodegradation route (DntB) we could trace a large share of ROS production to the first reaction of the route, which is executed by the multicomponent dioxygenase encoded by the dntA gene cluster. Naphthalene, the ancestral substrate of the dioxygenase from which DntA has evolved, also caused significant ROS formation. That both the old and the new substrate brought about a considerable cellular stress was indicative of a still-evolving DntA enzyme which is neither optimal any longer for naphthalene nor entirely advantageous yet for growth of the host strain on DNT. We could associate endogenous production of ROS with likely error-prone repair mechanisms of DNA damage, and the ensuing stress-induced mutagenesis in cells exposed to DNT. It is thus plausible that the evolutionary roadmap for biodegradation of xenobiotic compounds like DNT was largely elicited by mutagenic oxidative stress caused by faulty reactions of precursor enzymes with novel but structurally related substrates-to-be. Many bacteria have acquired the capacity of metabolizing chemical compounds that have never been in the Biosphere before the onset of contemporary synthetic chemistry. However, the factors that shape the new metabolic properties of such microorganisms remain obscure. We examined the performance of a still-evolving metabolic pathway for biodegradation of 2,4-dinitrotoluene (DNT, an archetypal xenobiotic compound) borne by a Burkholderia strain isolated from soil in an ammunition plant. The biodegradation pathway likely arose from a precursor set of genes for catabolism of naphthalene (although Burkholderia does not degrade this compound any longer), and is now advancing towards the new substrate, DNT. We found that the action of the first enzyme of the biodegradation pathway, a Rieske-type dioxygenase, on the still-suboptimal substrate (DNT) generates a high level of endogenous reactive oxygen species. This, in turn, damages DNA and increases mutagenesis, ultimately resulting in the creation of novelty that may foster evolution of xenobiotic-degrading variants of the strain hosting the biodegradation pathway. The very metabolic problem thus somehow seems to stimulate the exploration of the solution space. Our data is fully consistent with the notion that stress caused by faulty dioxygenation of DNT accelerates the rate of bacterial evolution.
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Affiliation(s)
- Danilo Pérez-Pantoja
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología, CSIC, Campus de Cantoblanco, Madrid, Spain
| | - Pablo I. Nikel
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología, CSIC, Campus de Cantoblanco, Madrid, Spain
| | - Max Chavarría
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología, CSIC, Campus de Cantoblanco, Madrid, Spain
| | - Víctor de Lorenzo
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología, CSIC, Campus de Cantoblanco, Madrid, Spain
- * E-mail:
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Moscoso F, Teijiz I, Sanromán MA, Deive FJ. On the Suitability of a Bacterial Consortium To Implement a Continuous PAHs Biodegradation Process in a Stirred Tank Bioreactor. Ind Eng Chem Res 2012. [DOI: 10.1021/ie3021736] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- F. Moscoso
- Department
of Chemical Engineering, University of Vigo, 36310 Vigo, Spain
| | - I. Teijiz
- Department
of Chemical Engineering, University of Vigo, 36310 Vigo, Spain
| | - M. A. Sanromán
- Department
of Chemical Engineering, University of Vigo, 36310 Vigo, Spain
| | - F. J. Deive
- Department
of Chemical Engineering, University of Vigo, 36310 Vigo, Spain
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36
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Moscoso F, Teijiz I, Deive FJ, Sanromán MA. Efficient PAHs biodegradation by a bacterial consortium at flask and bioreactor scale. BIORESOURCE TECHNOLOGY 2012; 119:270-6. [PMID: 22738812 DOI: 10.1016/j.biortech.2012.05.095] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2012] [Revised: 05/18/2012] [Accepted: 05/20/2012] [Indexed: 05/15/2023]
Abstract
In this work, the biodegradation of three polycyclic aromatic hydrocarbons (PAHs) such as Phenanthrene (PHE), Pyrene (PYR) and Benzo[a]anthracene (BaA) has been investigated. A bacterial consortium consisting of two strains was used for the first time based on preliminary promising biodegradation data. They were tentatively identified as Staphylococcus warneri and Bacillus pumilus. Degradation values higher than 85% were obtained for each single PAH when operating at flask scale, whereas minimum levels of 90% of PAHs removal were obtained after just 3 days of cultivation at bioreactor scale. The operation in cometabolic conditions led to maximum levels about 75% and 100% at flask and bioreactor scale, respectively. All the experimental data were analyzed in the light of logistic and Luedeking and Piret type models, with the purpose to better characterize the biodegradation process by S. warneri and B. pumilus. Finally, the metabolic pathway followed to degrade each PAH was ascertained.
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Affiliation(s)
- F Moscoso
- Department of Chemical Engineering, University of Vigo, 36310 Vigo, Spain
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Hahnke S, Tindall BJ, Schumann P, Sperling M, Brinkhoff T, Simon M. Planktotalea frisia gen. nov., sp. nov., isolated from the southern North Sea. Int J Syst Evol Microbiol 2012; 62:1619-1624. [DOI: 10.1099/ijs.0.033563-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A heterotrophic, aerobic bacterium, designated strain SH6-1T, was obtained from a seawater sample collected from the open North Sea during a phytoplankton bloom. Strain SH6-1T was isolated from a 10−6 dilution culture, which indicated a high abundance of this organism in the environmental sample. 16S rRNA gene sequence comparison revealed that strain SH6-1T belonged to the marine
Roseobacter
clade (order
Rhodobacterales
) within the class
Alphaproteobacteria
.
Pelagicola litoralis
CL-ES2T was the closest phylogenetic neighbour (96.4 % 16S rRNA gene sequence similarity). Cells of strain SH6-1T were small or elongated irregular rods. Optimal growth occurred between 20 and 25 °C and between pH 7.5 and 9.0 with peptone and yeast extract. On marine agar, the isolate formed non-pigmented, small, circular, convex colonies. For growth, cells required sodium ions and the vitamins pantothenic acid and nicotinic acid amide. The DNA G+C content was 53.8 mol%. The fatty acids (>1 %) were C10 : 0 3-OH, C16 : 0, C12 : 1, C12 : 1 3-OH, C18 : 0, C18 : 1ω7c, C18 : 2 and 11-methyl C18 : 1ω7c. The polar lipid pattern indicated the presence of phosphatidylcholine, phosphatidylglycerol, an unidentified aminolipid and one unidentified phospholipid. The major respiratory lipoquinone was ubiquinone Q-10. Strain SH6-1T contained the genes pufLM, which code for the bacterial photosynthesis reaction centre; however, no bacteriochlorophyll a could be detected. Physiological, genotypic and phenotypic differences from
P. litoralis
support the description of a novel genus and species, for which we suggest the name Planktotalea frisia gen. nov., sp. nov; the type strain of the type species is SH6-1T ( = DSM 23709T = LMG 25294T).
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Affiliation(s)
- Sarah Hahnke
- Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, D-26111 Oldenburg, Germany
| | - Brian J. Tindall
- DSMZ – Deutsche Sammlung von Mikroorganismen und Zellkulturen, Inhoffenstraße 7B, D-38124 Braunschweig, Germany
| | - Peter Schumann
- DSMZ – Deutsche Sammlung von Mikroorganismen und Zellkulturen, Inhoffenstraße 7B, D-38124 Braunschweig, Germany
| | - Martin Sperling
- Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, D-26111 Oldenburg, Germany
| | - Thorsten Brinkhoff
- Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, D-26111 Oldenburg, Germany
| | - Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, D-26111 Oldenburg, Germany
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Liu X, Gai Z, Tao F, Tang H, Xu P. Carotenoids play a positive role in the degradation of heterocycles by Sphingobium yanoikuyae. PLoS One 2012; 7:e39522. [PMID: 22745775 PMCID: PMC3380023 DOI: 10.1371/journal.pone.0039522] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Accepted: 05/22/2012] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Microbial oxidative degradation is a potential way of removing pollutants such as heterocycles from the environment. During this process, reactive oxygen species or other oxidants are inevitably produced, and may cause damage to DNA, proteins, and membranes, thereby decreasing the degradation rate. Carotenoids can serve as membrane-integrated antioxidants, protecting cells from oxidative stress. FINDINGS Several genes involved in the carotenoid biosynthetic pathway were cloned and characterized from a carbazole-degrading bacterium Sphingobium yanoikuyae XLDN2-5. In addition, a yellow-pigmented carotenoid synthesized by strain XLDN2-5 was identified as zeaxanthin that was synthesized from β-carotene through β-cryptoxanthin. The amounts of zeaxanthin and hydrogen peroxide produced were significantly and simultaneously enhanced during the biodegradation of heterocycles (carbazole < carbazole + benzothiophene < carbazole + dibenzothiophene). These higher production levels were consistent with the transcriptional increase of the gene encoding phytoene desaturase, one of the key enzymes for carotenoid biosynthesis. CONCLUSIONS/SIGNIFICANCE Sphingobium yanoikuyae XLDN2-5 can enhance the synthesis of zeaxanthin, one of the carotenoids, which may modulate membrane fluidity and defense against intracellular oxidative stress. To our knowledge, this is the first report on the positive role of carotenoids in the biodegradation of heterocycles, while elucidating the carotenoid biosynthetic pathway in the Sphingobium genus.
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Affiliation(s)
- Xiaorui Liu
- State Key Laboratory of Microbial Metabolism & School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People′s Republic of China
| | - Zhonghui Gai
- State Key Laboratory of Microbial Metabolism & School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People′s Republic of China
| | - Fei Tao
- State Key Laboratory of Microbial Metabolism & School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People′s Republic of China
| | - Hongzhi Tang
- State Key Laboratory of Microbial Metabolism & School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People′s Republic of China
| | - Ping Xu
- State Key Laboratory of Microbial Metabolism & School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People′s Republic of China
- * E-mail:
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Hahnke S, Tindall BJ, Schumann P, Simon M, Brinkhoff T. Pelagimonas varians gen. nov., sp. nov., isolated from the southern North Sea. Int J Syst Evol Microbiol 2012; 63:835-843. [PMID: 22611199 DOI: 10.1099/ijs.0.040675-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A heterotrophic, Gram-stain-negative, aerobic bacterium, designated strain SH4-1(T), was obtained from a seawater sample collected from the southern North Sea during a phytoplankton bloom. The 16S rRNA gene sequence comparison revealed affiliation to the Roseobacter clade (class Alphaproteobacteria) with Sulfitobacter marinus SW-265(T) as the most closely related characterized strain, showing 97.2 % 16S rRNA gene sequence similarity. Calculation of phylogenetic trees based on 16S rRNA gene sequences indicated, however, that members of the genus Roseobacter, Roseobacter denitrificans Och 114(T) and Roseobacter litoralis Och 149(T) (95 % and 96 % sequence similarity, respectively) fall between strain SH4-1(T) and the Sulfitobacter cluster including Oceanibulbus indolifex HEL-45(T) (≥95.4 % sequence similarity). Cells of strain SH4-1(T) are irregular rods with at least one flagellum. Optimal growth occurred between 28 and 32 °C and at a pH between 7.0 and 8.5. Cells require the vitamin nicotinic acid amide as well as sodium ions for growth. The DNA G+C content was 55.1 mol%. The fatty acids (>1 %) comprised C10 : 0 3-OH, C12 : 1, C14 : 1 3-OH, C16 : 0, C18 : 0, C18 : 2, C18 : 1ω7c and 11-methyl C18 : 1ω7c. The polar lipid pattern indicated the presence of phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylmonomethylethanolamine, an unidentified aminolipid, one unidentified phospholipid and one other unidentified lipid. On the basis of phenotypic, chemotaxonomic and phylogenetic differences, strain SH4-1(T) represents a novel species in a new genus within the family Rhodobacteraceae, for which we propose the name Pelagimonas varians gen. nov., sp. nov. The type strain of the type species is SH4-1(T) ( = DSM 23678(T) = LMG 26343(T) = CIP 110297(T)).
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Affiliation(s)
- Sarah Hahnke
- Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, D-26111 Oldenburg, Germany
| | - Brian J Tindall
- DSMZ - German Collection of Microorganisms and Cell Cultures, D-38124 Braunschweig, Germany
| | - Peter Schumann
- DSMZ - German Collection of Microorganisms and Cell Cultures, D-38124 Braunschweig, Germany
| | - Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, D-26111 Oldenburg, Germany
| | - Thorsten Brinkhoff
- Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, D-26111 Oldenburg, Germany
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Inorganic polyphosphates in extremophiles and their possible functions. Extremophiles 2012; 16:573-83. [PMID: 22585316 DOI: 10.1007/s00792-012-0457-9] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Accepted: 04/19/2012] [Indexed: 12/17/2022]
Abstract
Many extremophilic microorganisms are polyextremophiles, being confronted with more than one stress condition. For instance, some thermoacidophilic microorganisms are in addition capable to resist very high metal concentrations. Most likely, they have developed special adaptations to thrive in their living environments. Inorganic polyphosphate (polyP) is a molecule considered to be primitive in its origin and ubiquitous in nature. It has many roles besides being a reservoir for inorganic phosphate and energy. Of special interest are those functions related to survival under stressing conditions in all kinds of cells. PolyP may therefore have a fundamental part in extremophilic microorganism's endurance. Evidence for a role of polyP in the continued existence under acidic conditions, high concentrations of toxic heavy metals and elevated salt concentrations are reviewed in the present work. Actual evidence suggests that polyP may provide mechanistic alternatives in tuning microbial fitness for the adaptation under stressful environmental situations and may be of crucial relevance amongst extremophiles. The enzymes involved in polyP metabolism show structure conservation amongst bacteria and archaea. However, the lack of a canonical polyP synthase in Crenarchaea, which greatly accumulate polyP, strongly suggests that in this phylum a different enzyme may be in charge of its synthesis.
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41
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Moscoso F, Deive FJ, Longo MA, Sanromán MA. Technoeconomic assessment of phenanthrene degradation by Pseudomonas stutzeri CECT 930 in a batch bioreactor. BIORESOURCE TECHNOLOGY 2012; 104:81-89. [PMID: 22074903 DOI: 10.1016/j.biortech.2011.10.053] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2011] [Revised: 10/14/2011] [Accepted: 10/16/2011] [Indexed: 05/31/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are among the most persistent pollutants that accumulate in natural environment mainly as a result of anthropogenic activities. Therefore, the improvement of the available bank of microbial resources and information is crucial to the proper management of PAHs-polluted sites and effluents. In this work, Pseudomonas stutzeri CECT 930 was selected for aerobically degrading an aqueous effluent containing phenanthrene (PHE). Maximum PHE degradation of 90% was obtained both at flask and stirred tank bioreactor scale. All the experimental data were fitted to logistic and Luedeking and Piret models, and licensed to quantitatively ascertain a stronger dependence on the biomass of the metabolites triggering the bioremediation process. In addition, PHE degradation via protocatechuate pathway was elucidated through GC-MS data. Finally, based on the promising results of biodegradation, a preliminary economic evaluation of this process at industrial scale was approached by means of simulation data obtained with SuperPro Designer.
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Affiliation(s)
- F Moscoso
- Department of Chemical Engineering, University of Vigo, 36310 Vigo, Spain
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42
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Ponce BL, Latorre VK, González M, Seeger M. Antioxidant compounds improved PCB-degradation by Burkholderia xenovorans strain LB400. Enzyme Microb Technol 2011; 49:509-16. [DOI: 10.1016/j.enzmictec.2011.04.021] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Revised: 04/16/2011] [Accepted: 04/26/2011] [Indexed: 10/18/2022]
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Nemoto F, Kojima H, Fukui M. Diversity of freshwater Thioploca species and their specific association with filamentous bacteria of the phylum Chloroflexi. MICROBIAL ECOLOGY 2011; 62:753-764. [PMID: 21800088 DOI: 10.1007/s00248-011-9916-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2011] [Accepted: 07/13/2011] [Indexed: 05/31/2023]
Abstract
Phylogenetic diversity among filamentous sulfur-oxidizing bacteria of the genus Thioploca inhabiting freshwater/brackish environments was analyzed in detail. The 16S rRNA gene sequence of Thioploca found in a freshwater lake in Japan, Lake Okotanpe, was identical to that of Thioploca from Lake Ogawara, a brackish lake. The samples of the two lakes could be differentiated by the sequences of their 23S rRNA genes and 16S-23S rRNA internal transcribed spacer (ITS) regions. The 23S rRNA-based phylogenetic relationships between Thioploca samples from four lakes (Lake Okotanpe, Lake Ogawara, Lake Biwa, and Lake Constance) were similar to those based on the 16S rRNA gene sequences. In addition, multiple types of the ITS sequences were obtained from Thioploca inhabiting Lake Okotanpe and Lake Constance. Variations within respective Thioploca populations were also observed in the analysis of the soxB gene, involved in sulfur oxidation. As major members of the sheath-associated microbial community, bacteria of the phylum Chloroflexi were consistently detected in the samples from different lakes. Fluorescence in situ hybridization revealed that they were filamentous and abundantly distributed within the sheaths of Thioploca.
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Affiliation(s)
- Fumiko Nemoto
- The Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan
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Genomic analysis of the phenylacetyl-CoA pathway in Burkholderia xenovorans LB400. Arch Microbiol 2011; 193:641-50. [PMID: 21519854 DOI: 10.1007/s00203-011-0705-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2010] [Revised: 03/23/2011] [Accepted: 03/31/2011] [Indexed: 10/18/2022]
Abstract
The phenylacetyl-CoA (Paa) catabolic pathway and genome-wide gene expression responses to phenylacetate catabolism were studied in the polychlorinated biphenyl (PCB)-degrading strain Burkholderia xenovorans LB400. Microarray and RT-qPCR analyses identified three non-contiguous chromosomal clusters of genes that are predicted to encode a complete Paa pathway that were induced up to 40-fold during growth of LB400 on phenylacetate: paaGHIJKR, paaANEBDF, and paaC. Comparison of the available genome sequences revealed that this organization is unique to Burkholderiaceae. Parallel proteomic studies identified 7 of the 14 predicted Paa proteins, most of which were detected only in phenylacetate-grown cells, but not in benzoate- or succinate-grown cells. Finally, the transcriptomic and proteomic analyses revealed the induction of at least 7 predicted catabolic pathways of aromatic compounds and some aromatic plant products (phenols, mandelate, biphenyl, C(1) compounds, mevalonate, opine, and isoquinoline), as well as an oxidative stress response and a large group of transporters. Most of these genes were not induced during growth on benzoate or biphenyl, suggesting that phenylacetate or a metabolite may act as a signal that triggers multiple physiological processes. Identifying the components of the Paa pathway is important since the pathway appears to contribute to virulence of Burkholderia pathogens.
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45
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Fantino JR, Py B, Fontecave M, Barras F. A genetic analysis of the response of Escherichia coli to cobalt stress. Environ Microbiol 2011; 12:2846-57. [PMID: 20545747 DOI: 10.1111/j.1462-2920.2010.02265.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Cobalt can be toxic and the way cells adapt to its presence is largely unknown. Here we carried out a transcriptomic analysis of Escherichia coli exposed to cobalt. A limited number of genes were either up- or downregulated. Upregulated genes include the isc and the nfuA genes encoding Fe/S biogenesis assisting factors, and the rcnA gene encoding a cobalt efflux system. Downregulated genes are implicated in anaerobic metabolism (narK, nirB, hybO, grcA), metal transport (feoB, nikA), sulfate/thiosulfate import (cysP), and one is of unknown function (yeeE). Cobalt regulation of isc, nfuA, hybO, cysP and yeeE genes was found to involve IscR, a Fe/S transcriptional regulator. Previously, the Suf Fe/S biogenesis machinery was found to be important for cobalt stress adaptation, but suf genes did not show up in the microarray analysis. Therefore, we used qRT-PCR analysis and found that cobalt induced the suf operon expression. Moreover, kinetic analysis of the cobalt-mediated induction of the suf operon expression allowed us to propose that cobalt toxicity is caused first by impaired Fe/S biogenesis, followed by decreased iron bioavailability and eventually oxidative stress.
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Affiliation(s)
- Jean-Raphaël Fantino
- Laboratoire de Chimie Bactérienne, CNRS UPR-9043, Institut de Microbiologie de la Méditerranée, 31 Chemin Joseph Aiguier, 13009 Marseille, France
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46
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Puglisi E, Cahill MJ, Lessard PA, Capri E, Sinskey AJ, Archer JAC, Boccazzi P. Transcriptional response of Rhodococcus aetherivorans I24 to polychlorinated biphenyl-contaminated sediments. MICROBIAL ECOLOGY 2010; 60:505-515. [PMID: 20369357 DOI: 10.1007/s00248-010-9650-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2009] [Accepted: 02/22/2010] [Indexed: 05/29/2023]
Abstract
We used a microarray targeting 3,524 genes to assess the transcriptional response of the actinomycete Rhodococcus aetherivorans I24 in minimal medium supplemented with various substrates (e.g., PCBs) and in both PCB-contaminated and non-contaminated sediment slurries. Relative to the reference condition (minimal medium supplemented with glucose), 408 genes were upregulated in the various treatments. In medium and in sediment, PCBs elicited the upregulation of a common set of 100 genes, including gene-encoding chaperones (groEL), a superoxide dismutase (sodA), alkyl hydroperoxide reductase protein C (ahpC), and a catalase/peroxidase (katG). Analysis of the R. aetherivorans I24 genome sequence identified orthologs of many of the genes in the canonical biphenyl pathway, but very few of these genes were upregulated in response to PCBs or biphenyl. This study is one of the first to use microarrays to assess the transcriptional response of a soil bacterium to a pollutant under conditions that more closely resemble the natural environment. Our results indicate that the transcriptional response of R. aetherivorans I24 to PCBs, in both medium and sediment, is primarily directed towards reducing oxidative stress, rather than catabolism.
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Affiliation(s)
- Edoardo Puglisi
- Istituto di Chimica Agraria ed Ambientale, Università Cattolica del Sacro Cuore, Piacenza, Italy
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Tremaroli V, Vacchi Suzzi C, Fedi S, Ceri H, Zannoni D, Turner RJ. Tolerance of Pseudomonas pseudoalcaligenes KF707 to metals, polychlorobiphenyls and chlorobenzoates: effects on chemotaxis-, biofilm- and planktonic-grown cells. FEMS Microbiol Ecol 2010; 74:291-301. [PMID: 20846140 DOI: 10.1111/j.1574-6941.2010.00965.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Pseudomonas pseudoalcaligenes KF707 is a polychlorinated biphenyls (PCBs) degrader, also tolerant to several toxic metals and metalloids. The work presented here examines for the first time the chemotactic response of P. pseudoalcaligenes KF707 to biphenyl and intermediates of the PCB biodegradation pathway in the presence and absence of metals. Chemotaxis analyses showed that biphenyl, benzoic acid and chlorobenzoic acids acted as chemoattractants for KF707 cells and that metal cations such as Ni(2+) and Cu(2+) strongly affected the chemotactic response. Toxicity profiles of various metals on KF707 cells grown on succinate or biphenyl as planktonic and biofilm were determined both in the presence and in the absence of PCBs. Notably, KF707 cells from both biofilms and planktonic cultures were tolerant to high amounts (up to 0.5 g L(-1)) of Aroclor 1242, a commercial mixture of PCBs. Together, the data show that KF707 cells are chemotactic and can form a biofilm in the presence of Aroclor 1242 and specific metals. These findings provide new perspectives on the effectiveness of using PCB-degrading bacterial strains in bioremediation strategies of metal-co-contaminated sites.
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Affiliation(s)
- Valentina Tremaroli
- Department of Biology, General Microbiology Unit, University of Bologna, Bologna, Italy
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Varela C, Mauriaca C, Paradela A, Albar JP, Jerez CA, Chávez FP. New structural and functional defects in polyphosphate deficient bacteria: a cellular and proteomic study. BMC Microbiol 2010; 10:7. [PMID: 20067623 PMCID: PMC2817675 DOI: 10.1186/1471-2180-10-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2009] [Accepted: 01/12/2010] [Indexed: 12/15/2022] Open
Abstract
Background Inorganic polyphosphate (polyP), a polymer of tens or hundreds of phosphate residues linked by ATP-like bonds, is found in all organisms and performs a wide variety of functions. PolyP is synthesized in bacterial cells by the actions of polyphosphate kinases (PPK1 and PPK2) and degraded by exopolyphosphatase (PPX). Bacterial cells with polyP deficiencies due to knocking out the ppk1 gene are affected in many structural and important cellular functions such as motility, quorum sensing, biofilm formation and virulence among others. The cause of this pleiotropy is not entirely understood. Results The overexpression of exopolyphosphatase in bacteria mimicked some pleitropic defects found in ppk1 mutants. By using this approach we found new structural and functional defects in the polyP-accumulating bacteria Pseudomonas sp. B4, which are most likely due to differences in the polyP-removal strategy. Colony morphology phenotype, lipopolysaccharide (LPS) structure changes and cellular division malfunction were observed. Finally, we used comparative proteomics in order to elucidate the cellular adjustments that occurred during polyP deficiency in this bacterium and found some clues that helped to understand the structural and functional defects observed. Conclusions The results obtained suggest that during polyP deficiency energy metabolism and particularly nucleoside triphosphate (NTP) formation were affected and that bacterial cells overcame this problem by increasing the flux of energy-generating metabolic pathways such as tricarboxilic acid (TCA) cycle, β-oxidation and oxidative phosphorylation and by reducing energy-consuming ones such as active transporters and amino acid biosynthesis. Furthermore, our results suggest that a general stress response also took place in the cell during polyP deficiency.
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Affiliation(s)
- Cristian Varela
- Department of Biology, Faculty of Sciences, Laboratory of Molecular Microbiology and Biotechnology & Millennium Institute of Cell Dynamics and Biotechnology, University of Chile, Las Palmeras 3425, Nuñoa, Santiago, Chile
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Lee IJ, Kim KW, Hyun JW, Lee YH, Park EW. Comparative ultrastructure of nonwounded Mexican lime and Yuzu leaves infected with the citrus canker bacterium Xanthomonas citri pv. citri. Microsc Res Tech 2009; 72:507-16. [PMID: 19291686 DOI: 10.1002/jemt.20707] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Ultrastructural aspects of citrus canker development were investigated in nonwounded leaves of citrus species by transmission electron microscopy (TEM). A susceptible species Mexican lime and a resistant species Yuzu were spray-inoculated with a virulent strain of Xanthomonas citri pv. citri. Initial symptoms occurred on Mexican lime approximately 9 days after inoculation, whereas they appeared on Yuzu mostly 11 days after inoculation. In Mexican lime leaves, the bacterial invasion was usually accompanied by host cell wall dissolution and cellular disruption. Fibrillar materials from degenerated cell walls were usually found in intercellular spaces. Damaged host cells with necrotic cytoplasm showed the localized separation of plasma membrane from the cell wall. Bacterial multiplication and electron-transparent capsule-like structures around bacteria were commonly observed. Meanwhile, cell wall protuberances were prominent outside host cell walls in response to bacterial invasion in Yuzu leaves. Occlusion of intercellular spaces was also formed by the fusion of two or more individual cell wall protuberances originated from two adjacent host cells. Papillae-like materials accumulated locally within host cells in close proximity to bacteria. Some bacteria were found to be undergoing degeneration in xylem vessels. Also, the shrunken, inactive bacteria were surrounded by electron-translucent fibrillar materials in intercellular spaces, implying bacterial immobilization. These cellular responses are thought to be the consequences of defense responses of Yuzu leaves to invading bacteria. In both citrus species, X. citri pv. citri contained polyphosphate bodies showing electron-dense and elliptical structures in cytoplasm.
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Affiliation(s)
- In Jung Lee
- Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea
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50
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Cell envelope perturbation induces oxidative stress and changes in iron homeostasis in Vibrio cholerae. J Bacteriol 2009; 191:5398-408. [PMID: 19542276 DOI: 10.1128/jb.00092-09] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The Vibrio cholerae type II secretion (T2S) machinery is a multiprotein complex that spans the cell envelope. When the T2S system is inactivated, cholera toxin and other exoproteins accumulate in the periplasmic compartment. Additionally, loss of secretion via the T2S system leads to a reduced growth rate, compromised outer membrane integrity, and induction of the extracytoplasmic stress factor RpoE (A. E. Sikora, S. R. Lybarger, and M. Sandkvist, J. Bacteriol. 189:8484-8495, 2007). In this study, gene expression profiling reveals that inactivation of the T2S system alters the expression of genes encoding cell envelope components and proteins involved in central metabolism, chemotaxis, motility, oxidative stress, and iron storage and acquisition. Consistent with the gene expression data, molecular and biochemical analyses indicate that the T2S mutants suffer from internal oxidative stress and increased levels of intracellular ferrous iron. By using a tolA mutant of V. cholerae that shares a similar compromised membrane phenotype but maintains a functional T2S machinery, we show that the formation of radical oxygen species, induction of oxidative stress, and changes in iron physiology are likely general responses to cell envelope damage and are not unique to T2S mutants. Finally, we demonstrate that disruption of the V. cholerae cell envelope by chemical treatment with polymyxin B similarly results in induction of the RpoE-mediated stress response, increased sensitivity to oxidants, and a change in iron metabolism. We propose that many types of extracytoplasmic stresses, caused either by genetic alterations of outer membrane constituents or by chemical or physical damage to the cell envelope, induce common signaling pathways that ultimately lead to internal oxidative stress and misregulation of iron homeostasis.
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