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Cyriaque V, Ibarra-Chávez R, Kuchina A, Seelig G, Nesme J, Madsen JS. Single-cell RNA sequencing reveals plasmid constrains bacterial population heterogeneity and identifies a non-conjugating subpopulation. Nat Commun 2024; 15:5853. [PMID: 38997267 PMCID: PMC11245611 DOI: 10.1038/s41467-024-49793-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 06/18/2024] [Indexed: 07/14/2024] Open
Abstract
Transcriptional heterogeneity in isogenic bacterial populations can play various roles in bacterial evolution, but its detection remains technically challenging. Here, we use microbial split-pool ligation transcriptomics to study the relationship between bacterial subpopulation formation and plasmid-host interactions at the single-cell level. We find that single-cell transcript abundances are influenced by bacterial growth state and plasmid carriage. Moreover, plasmid carriage constrains the formation of bacterial subpopulations. Plasmid genes, including those with core functions such as replication and maintenance, exhibit transcriptional heterogeneity associated with cell activity. Notably, we identify a cell subpopulation that does not transcribe conjugal plasmid transfer genes, which may help reduce plasmid burden on a subset of cells. Our study advances the understanding of plasmid-mediated subpopulation dynamics and provides insights into the plasmid-bacteria interplay.
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Affiliation(s)
- Valentine Cyriaque
- Section of Microbiology, University of Copenhagen, Copenhagen, Denmark.
- Proteomics and Microbiology Laboratory, Research Institute for Biosciences, UMONS, Mons, Belgium.
| | | | - Anna Kuchina
- Institute for Systems Biology, Seattle, WA, USA
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA, USA
- Department of Electrical and Computer Engineering, University of Washington, Seattle, WA, USA
| | - Georg Seelig
- Department of Electrical and Computer Engineering, University of Washington, Seattle, WA, USA
- Paul G. Allen School for Computer Science & Engineering, University of Washington, Seattle, WA, USA
| | - Joseph Nesme
- Section of Microbiology, University of Copenhagen, Copenhagen, Denmark
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2
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Moreno R, Yuste L, Morales G, Rojo F. Inactivation of Pseudomonas putida KT2440 pyruvate dehydrogenase relieves catabolite repression and improves the usefulness of this strain for degrading aromatic compounds. Microb Biotechnol 2024; 17:e14514. [PMID: 38923400 PMCID: PMC11196380 DOI: 10.1111/1751-7915.14514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 06/09/2024] [Indexed: 06/28/2024] Open
Abstract
Pyruvate dehydrogenase (PDH) catalyses the irreversible decarboxylation of pyruvate to acetyl-CoA, which feeds the tricarboxylic acid cycle. We investigated how the loss of PDH affects metabolism in Pseudomonas putida. PDH inactivation resulted in a strain unable to utilize compounds whose assimilation converges at pyruvate, including sugars and several amino acids, whereas compounds that generate acetyl-CoA supported growth. PDH inactivation also resulted in the loss of carbon catabolite repression (CCR), which inhibits the assimilation of non-preferred compounds in the presence of other preferred compounds. Pseudomonas putida can degrade many aromatic compounds, most of which produce acetyl-CoA, making it useful for biotransformation and bioremediation. However, the genes involved in these metabolic pathways are often inhibited by CCR when glucose or amino acids are also present. Our results demonstrate that the PDH-null strain can efficiently degrade aromatic compounds even in the presence of other preferred substrates, which the wild-type strain does inefficiently, or not at all. As the loss of PDH limits the assimilation of many sugars and amino acids and relieves the CCR, the PDH-null strain could be useful in biotransformation or bioremediation processes that require growth with mixtures of preferred substrates and aromatic compounds.
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Affiliation(s)
- Renata Moreno
- Department of Microbial BiotechnologyCentro Nacional de Biotecnología, CSICMadridSpain
| | - Luis Yuste
- Department of Microbial BiotechnologyCentro Nacional de Biotecnología, CSICMadridSpain
| | - Gracia Morales
- Department of Microbial BiotechnologyCentro Nacional de Biotecnología, CSICMadridSpain
- Present address:
European UniversityMadridSpain
| | - Fernando Rojo
- Department of Microbial BiotechnologyCentro Nacional de Biotecnología, CSICMadridSpain
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3
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Genetic Characterization of the Ibuprofen-Degradative Pathway of Rhizorhabdus wittichii MPO218. Appl Environ Microbiol 2022; 88:e0038822. [PMID: 35604231 PMCID: PMC9195938 DOI: 10.1128/aem.00388-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ibuprofen is one of the most common drugs found as a contaminant in soils, sediments, and waters. Although several microorganisms able to metabolize ibuprofen have been described, the metabolic pathways and factors limiting biodegradation in nature remain poorly characterized. Among the bacteria able to grow on ibuprofen, three different strains belonging to Sphingomonadaceae and isolated from different geographical locations carry the same set of genes required for the upper part of the ibuprofen metabolic pathway. Here, we have studied the metabolic pathway of Rhizorhabdus wittichii MPO218, identifying new genes required for the lower part of the ibuprofen metabolic pathway. We have identified two new DNA regions in MPO218 involved in the metabolism of ibuprofen. One is located on the MPO218 chromosome and appears to be required for the metabolism of propionyl-CoA through the methylmalonyl-CoA pathway. Although involved in ibuprofen metabolism, this region is not strictly necessary for growing using ibuprofen. The second region belongs to the pIBU218 plasmid and comprises two gene clusters containing aromatic compound biodegradation genes, part of which are necessary for ibuprofen degradation. We have identified two genes required for the first two steps of the lower part of the ibuprofen metabolic pathway (ipfL and ipfM), and, based on our results, we propose the putative complete pathway for ibuprofen metabolism in strain MPO218. IMPORTANCE Ibuprofen, one of the most common pharmaceutical contaminants in natural environments, is toxic for some aquatic and terrestrial organisms. The main source of environmental ibuprofen is wastewater, so improving wastewater treatment is of relevant importance. Although several microorganisms capable of biodegrading ibuprofen have been described, the metabolic pathways and their genetic bases remain poorly understood. Three bacterial strains of the family Sphingomonadaceae capable of using ibuprofen as carbon and energy source have been described. Although the genes involved in the upper part of the degradation pathway (ipfABDEF cluster) have been identified, those required for the lower part of the pathway remained unknown. Here, we have confirmed the requirement of the ipf cluster for the generation of isobutyl catechol and have identified the genes involved in the subsequent transformation of the metabolic products. Identification of genes involved in ibuprofen degradation is essential to developing improved strains for the removal of this contaminant.
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4
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Marcon L, Oliveras J, Puntes VF. In situ nanoremediation of soils and groundwaters from the nanoparticle's standpoint: A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 791:148324. [PMID: 34412401 DOI: 10.1016/j.scitotenv.2021.148324] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 05/21/2021] [Accepted: 06/04/2021] [Indexed: 06/13/2023]
Abstract
Anthropogenic pollution coming from industrial processes, agricultural practices and consumer products, results in the release of toxic substances into rural and urban environments. Once released, these chemicals migrate through the atmosphere and water, and find their way into matrices such as sediments and groundwaters, thus making large areas potentially uninhabitable. Common pollutants, including heavy metal(loid)s, radionuclides, aliphatic hydrocarbons and halogenated organics, are known to adversely affect physiological systems in animal species. Pollution can be cleaned up using techniques such as coagulation, reverse osmosis, oxidation and biological methods, among others. The use of nanoparticles (NPs) extends the range of available technologies and offers particular benefits, not only by degrading, transforming and immobilizing contaminants, but also by reaching inaccessible areas and promoting biotic degradation. The development of NPs is understandably heralded as an environmentally beneficial technology; however, it is only now that the ecological risks associated with their use are being evaluated. This review presents recent developments in the use of engineered NPs for the in situ remediation of two paramount environmental matrices: soils and groundwaters. Emphasis will be placed on (i) the successful applications of nano-objects for environmental cleanup, (ii) the potential safety implications caused by the challenging requirements of [high reactivity toward pollutants] vs. [none reactivity toward biota], with a thorough view on their transport and evolution in the matrix, and (iii) the perspectives on scientific and regulatory challenges. To this end, the most promising nanomaterials will be considered, including nanoscale zerovalent iron, nano-oxides and carbonaceous materials. The purpose of the present review is to give an overview of the development of nanoremediators since they appeared in the 2000s, from their chemical modifications, mechanism of action and environmental behavior to an understanding of the problematics (technical limitations, economic constraints and institutional precautionary approaches) that will drive their future full-scale applications.
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Affiliation(s)
- Lionel Marcon
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes (LBBM) USR CNRS 3579, Observatoire Océanologique, F-66650 Banyuls/Mer, France; Université de Perpignan Via Domitia, Biocapteurs-Analyses-Environnement, 66860 Perpignan, France.
| | - Jana Oliveras
- Institut Català de Nanociència i Nanotecnologia (ICN2), Campus de la Universitat Autònoma de Barcelona (Campus UAB), 08193, Bellaterra, Barcelona, Spain; Universitat Autònoma de Barcelona (UAB), Campus UAB, 08193, Bellaterra, Barcelona, Catalonia, Spain
| | - Víctor F Puntes
- Institut Català de Nanociència i Nanotecnologia (ICN2), Campus de la Universitat Autònoma de Barcelona (Campus UAB), 08193, Bellaterra, Barcelona, Spain; Vall d'Hebron Institut de Recerca (VHIR), Edificio Mediterránea, Hospital Vall d'Hebron, Passeig de la Vall d'Hebron, 119-129, 08035 Barcelona, Spain; Institut Català de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys, 23, 08010 Barcelona, Spain
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5
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Gómez-García G, Ruiz-Enamorado A, Yuste L, Rojo F, Moreno R. Expression of the ISPpu9 transposase of Pseudomonas putida KT2440 is regulated by two small RNAs and the secondary structure of the mRNA 5'-untranslated region. Nucleic Acids Res 2021; 49:9211-9228. [PMID: 34379788 PMCID: PMC8450116 DOI: 10.1093/nar/gkab672] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 06/23/2021] [Accepted: 07/26/2021] [Indexed: 11/20/2022] Open
Abstract
Insertion sequences (ISs) are mobile genetic elements that only carry the information required for their own transposition. Pseudomonas putida KT2440, a model bacterium, has seven copies of an IS called ISPpu9 inserted into repetitive extragenic palindromic sequences. This work shows that the gene for ISPpu9 transposase, tnp, is regulated by two small RNAs (sRNAs) named Asr9 and Ssr9, which are encoded upstream and downstream of tnp, respectively. The tnp mRNA has a long 5′-untranslated region (5′-UTR) that can fold into a secondary structure that likely includes the ribosome-binding site (RBS). Mutations weakening this structure increased tnp mRNA translation. Asr9, an antisense sRNA complementary to the 5′-UTR, was shown to be very stable. Eliminating Asr9 considerably reduced tnp mRNA translation, suggesting that it helps to unfold this secondary structure, exposing the RBS. Ectopic overproduction of Asr9 increased the transposition frequency of a new ISPpu9 entering the cell by conjugation, suggesting improved tnp expression. Ssr9 has significant complementarity to Asr9 and annealed to it in vitro forming an RNA duplex; this would sequester it and possibly facilitate its degradation. Thus, the antisense Asr9 sRNA likely facilitates tnp expression, improving transposition, while Ssr9 might counteract Asr9, keeping tnp expression low.
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Affiliation(s)
- Guillermo Gómez-García
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CSIC, Madrid 28049, Spain
| | - Angel Ruiz-Enamorado
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CSIC, Madrid 28049, Spain
| | - Luis Yuste
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CSIC, Madrid 28049, Spain
| | - Fernando Rojo
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CSIC, Madrid 28049, Spain
| | - Renata Moreno
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CSIC, Madrid 28049, Spain
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6
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Arce-Rodríguez A, Nikel PI, Calles B, Chavarría M, Platero R, Krell T, de Lorenzo V. Low CyaA expression and anti-cooperative binding of cAMP to CRP frames the scope of the cognate regulon of Pseudomonas putida. Environ Microbiol 2021; 23:1732-1749. [PMID: 33559269 DOI: 10.1111/1462-2920.15422] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 01/09/2021] [Accepted: 02/02/2021] [Indexed: 12/29/2022]
Abstract
Although the soil bacterium Pseudomonas putida KT2440 bears a bona fide adenylate cyclase gene (cyaA), intracellular concentrations of 3',5'-cyclic adenosine monophosphate (cAMP) are barely detectable. By using reporter technology and direct quantification of cAMP under various conditions, we show that such low levels of the molecule stem from the stringent regulation of its synthesis, efflux and degradation. Poor production of cAMP was the result of inefficient translation of cyaA mRNA. Moreover, deletion of the cAMP-phosphodiesterase pde gene led to intracellular accumulation of the cyclic nucleotide, exposing an additional cause of cAMP drain in vivo. But even such low levels of the signal sustained activation of promoters dependent on the cAMP-receptor protein (CRP). Genetic and biochemical evidence indicated that the phenomenon ultimately rose from the unusual binding parameters of cAMP to CRP. This included an ultratight cAMP-CrpP. putida affinity (KD of 45.0 ± 3.4 nM) and an atypical 1:1 effector/dimer stoichiometry that obeyed an infrequent anti-cooperative binding mechanism. It thus seems that keeping the same regulatory parts and their relational logic but changing the interaction parameters enables genetic devices to take over entirely different domains of the functional landscape.
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Affiliation(s)
- Alejandro Arce-Rodríguez
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, 38124, Germany
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, 2800, Denmark
| | - Belén Calles
- Systems Biology Department, Centro Nacional de Biotecnología-CSIC, Campus de Cantoblanco, Madrid, 28049, Spain
| | - Max Chavarría
- Escuela de Química and CIPRONA, Universidad de Costa Rica, San José, 2060, Costa Rica
| | - Raúl Platero
- Departamento de Bioquímica y Genómica Microbianas, Instituto de Investigaciones Biológicas Clemente Estable, MEC, Montevideo, Uruguay
| | - Tino Krell
- Department of Environmental Protection, Estación Experimental del Zaidín CSIC, Granada, 18008, Spain
| | - Victor de Lorenzo
- Systems Biology Department, Centro Nacional de Biotecnología-CSIC, Campus de Cantoblanco, Madrid, 28049, Spain
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7
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Identification of two fnr genes and characterisation of their role in the anaerobic switch in Sphingopyxis granuli strain TFA. Sci Rep 2020; 10:21019. [PMID: 33273546 PMCID: PMC7713065 DOI: 10.1038/s41598-020-77927-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 11/17/2020] [Indexed: 11/16/2022] Open
Abstract
Sphingopyxis granuli strain TFA is able to grow on the organic solvent tetralin as the only carbon and energy source. The aerobic catabolic pathway for tetralin, the genes involved and their regulation have been fully characterised. Unlike most of the bacteria belonging to the sphingomonads group, this strain is able to grow in anoxic conditions by respiring nitrate, though not nitrite, as the alternative electron acceptor. In this work, two fnr-like genes, fnrN and fixK, have been identified in strain TFA. Both genes are functional in E. coli and Sphingopyxis granuli although fixK, whose expression is apparently activated by FnrN, seems to be much less effective than fnrN in supporting anaerobic growth. Global transcriptomic analysis of a ΔfnrN ΔfixK double mutant and identification of Fnr boxes have defined a minimal Fnr regulon in this bacterium. However, expression of a substantial number of anaerobically regulated genes was not affected in the double mutant. Additional regulators such regBA, whose expression is also activated by Fnr, might also be involved in the anaerobic response. Anaerobically induced stress response genes were not regulated by Fnr but apparently induced by stress conditions inherent to anaerobic growth, probably due to accumulation of nitrite and nitric oxide.
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8
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López-Lara LI, Pazos-Rojas LA, López-Cruz LE, Morales-García YE, Quintero-Hernández V, de la Torre J, van Dillewijn P, Muñoz-Rojas J, Baez A. Influence of rehydration on transcriptome during resuscitation of desiccated Pseudomonas putida KT2440. ANN MICROBIOL 2020. [DOI: 10.1186/s13213-020-01596-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Abstract
Purpose
Pseudomonas putida KT2440 is a desiccation-sensitive bacterium that loses culturability after 15 days of air desiccation. We have previously shown that P. putida KT2440 can develop a viable but nonculturable (VBNC) state after being exposed to desiccation stress and eventually recover when desiccated cells are rehydrated for at least 24 h.
Methods
To determine which genes of transport, oxidation-reduction, and transcription processes could be involved in the return of P. putida KT2440 to the culturable state, a transcriptome analysis was carried out comparing the gene expression of non-desiccated samples with samples subjected to desiccation followed by 20 min of rehydration or desiccation followed by 24 h of rehydration.
Results
Desiccation stress triggered a VBNC state of P. putida. The major response was detected after 24 h of rehydration with 148 upregulated and 42 downregulated genes. During the VBNC state, P. putida activated transmembrane transport processes like that of siderophores through a TonB-dependent transporter and putative polyhydric alcohol transport systems. Prolonged rehydration with distilled water resuscitated P. putida KT2440 cells activating the catabolism of phenylalanine/tyrosine to provide energy and carbon for ubiquinone biosynthesis while maintaining a reduced protein synthesis. On the other hand, the interruption of the TonB-dependent receptor gene (PP_1446) increased desiccation survival of the mutant strain.
Conclusion
The activation of the iron transport system (TonB-dependent siderophore receptor) and alcohol transport can be helping the VBNC state of P. putida. Activation of catabolism of phenylalanine/tyrosine and reduced protein synthesis was needed for resuscitation from the VBNC state.
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Nakamura T, Suzuki-Minakuchi C, Kawano H, Kanesaki Y, Kawasaki S, Okada K, Nojiri H. H-NS Family Proteins Drastically Change Their Targets in Response to the Horizontal Transfer of the Catabolic Plasmid pCAR1. Front Microbiol 2020; 11:1099. [PMID: 32547524 PMCID: PMC7273181 DOI: 10.3389/fmicb.2020.01099] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Accepted: 05/04/2020] [Indexed: 01/20/2023] Open
Abstract
H-NS family proteins regulate the expression of many genes by preferably binding to AT-rich genomic regions and altering DNA topology. They are found in both bacterial chromosomes and plasmids, and plasmid-encoded H-NS family proteins have sometimes been suggested to act as a molecular backup of the chromosomally encoded ones. Pmr is an H-NS family protein encoded on the catabolic plasmid pCAR1, which belongs to incompatibility P-7 group. We have investigated the function of Pmr in Pseudomonas putida KT2440, where two H-NS family proteins (TurA and TurB) encoded on the chromosome are expressed predominantly. Previous transcriptome analyses suggested that TurA, TurB, and Pmr cooperatively regulate numerous genes, but the differentially transcribed genes in KT2440ΔturA(pCAR1), KT2440ΔturB(pCAR1), and KT2440(pCAR1Δpmr) compared with those in KT2440(pCAR1) were somewhat different. Here, we performed RNA sequencing analyses to compare the differentially transcribed genes after the deletion of turA or turB in KT2440, and turA, turB or pmr in KT2440(pCAR1). Three pCAR1-free strains (KT2440, KT2440ΔturA, KT2440ΔturB) and four pCAR1-harboring strains [KT2440(pCAR1), KT2440ΔturA(pCAR1), KT2440ΔturB(pCAR1), KT2440(pCAR1Δpmr)], grown until the log and stationary phases, were used. In KT2440, TurA was the major H-NS family protein regulating a large number and wide range of genes, and both TurA and TurB were suggested to functionally compensate each other, particularly during the stationary phase. In KT2440(pCAR1), the numbers of differentially transcribed genes after the deletion of turA or turB drastically increased compared to those in KT2440. Notably, more than half of the differentially transcribed genes in KT2440ΔturA and KT2440ΔturB did not overlap with those in KT2440ΔturA(pCAR1) and KT2440ΔturB(pCAR1). This dynamic change could be explained by the acquisition of pCAR1 itself and the expression of Pmr. After pCAR1 was transferred into the host, TurA and TurB could be detached from the chromosome of KT2440 and they could newly bind to pCAR1. Moreover, Pmr could reconstitute the chromosome-binding heteromeric oligomers which were formed by TurA and TurB. Our study revealed that horizontal transfer of a plasmid changes the transcriptional network of the chromosomally encoded H-NS family proteins.
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Affiliation(s)
- Taisuke Nakamura
- Biotechnology Research Center, The University of Tokyo, Tokyo, Japan
| | - Chiho Suzuki-Minakuchi
- Biotechnology Research Center, The University of Tokyo, Tokyo, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
| | - Hibiki Kawano
- Biotechnology Research Center, The University of Tokyo, Tokyo, Japan
| | - Yu Kanesaki
- NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo, Japan
| | - Shinji Kawasaki
- Department of Molecular Microbiology, Tokyo University of Agriculture, Tokyo, Japan
| | - Kazunori Okada
- Biotechnology Research Center, The University of Tokyo, Tokyo, Japan
| | - Hideaki Nojiri
- Biotechnology Research Center, The University of Tokyo, Tokyo, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
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10
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de Dios R, Rivas-Marin E, Santero E, Reyes-Ramírez F. Two paralogous EcfG σ factors hierarchically orchestrate the activation of the General Stress Response in Sphingopyxis granuli TFA. Sci Rep 2020; 10:5177. [PMID: 32198475 PMCID: PMC7083833 DOI: 10.1038/s41598-020-62101-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 02/20/2020] [Indexed: 12/15/2022] Open
Abstract
Under ever-changing environmental conditions, the General Stress Response (GSR) represents a lifesaver for bacteria in order to withstand hostile situations. In α-proteobacteria, the EcfG-type extracytoplasmic function (ECF) σ factors are the key activators of this response at the transcriptional level. In this work, we address the hierarchical function of the ECF σ factor paralogs EcfG1 and EcfG2 in triggering the GSR in Sphingopyxis granuli TFA and describe the role of EcfG2 as global switch of this response. In addition, we define a GSR regulon for TFA and use in vitro transcription analysis to study the relative contribution of each EcfG paralog to the expression of selected genes. We show that the features of each promoter ultimately dictate this contribution, though EcfG2 always produced more transcripts than EcfG1 regardless of the promoter. These first steps in the characterisation of the GSR in TFA suggest a tight regulation to orchestrate an adequate protective response in order to survive in conditions otherwise lethal.
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Affiliation(s)
- Rubén de Dios
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide/Consejo Superior de Investigaciones Científicas/Junta de Andalucía. Departamento de Biología Molecular e Ingeniería Bioquímica, Seville, Spain
| | - Elena Rivas-Marin
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide/Consejo Superior de Investigaciones Científicas/Junta de Andalucía. Departamento de Biología Molecular e Ingeniería Bioquímica, Seville, Spain
| | - Eduardo Santero
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide/Consejo Superior de Investigaciones Científicas/Junta de Andalucía. Departamento de Biología Molecular e Ingeniería Bioquímica, Seville, Spain
| | - Francisca Reyes-Ramírez
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide/Consejo Superior de Investigaciones Científicas/Junta de Andalucía. Departamento de Biología Molecular e Ingeniería Bioquímica, Seville, Spain.
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11
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Abstract
Pseudomonas putidais a fast-growing bacterium found mostly in temperate soil and water habitats. The metabolic versatility ofP. putidamakes this organism attractive for biotechnological applications such as biodegradation of environmental pollutants and synthesis of added-value chemicals (biocatalysis). This organism has been extensively studied in respect to various stress responses, mechanisms of genetic plasticity and transcriptional regulation of catabolic genes.P. putidais able to colonize the surface of living organisms, but is generally considered to be of low virulence. A number ofP. putidastrains are able to promote plant growth. The aim of this review is to give historical overview of the discovery of the speciesP. putidaand isolation and characterization ofP. putidastrains displaying potential for biotechnological applications. This review also discusses some major findings inP. putidaresearch encompassing regulation of catabolic operons, stress-tolerance mechanisms and mechanisms affecting evolvability of bacteria under conditions of environmental stress.
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12
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Rivas-Marin E, Peeters SH, Claret Fernández L, Jogler C, van Niftrik L, Wiegand S, Devos DP. Non-essentiality of canonical cell division genes in the planctomycete Planctopirus limnophila. Sci Rep 2020; 10:66. [PMID: 31919386 PMCID: PMC6952346 DOI: 10.1038/s41598-019-56978-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 12/19/2019] [Indexed: 12/13/2022] Open
Abstract
Most bacteria divide by binary fission using an FtsZ-based mechanism that relies on a multi-protein complex, the divisome. In the majority of non-spherical bacteria another multi-protein complex, the elongasome, is also required for the maintenance of cell shape. Components of these multi-protein assemblies are conserved and essential in most bacteria. Here, we provide evidence that at least three proteins of these two complexes are not essential in the FtsZ-less ovoid planctomycete bacterium Planctopirus limnophila which divides by budding. We attempted to construct P. limnophila knock-out mutants of the genes coding for the divisome proteins FtsI, FtsK, FtsW and the elongasome protein MreB. Surprisingly, ftsI, ftsW and mreB could be deleted without affecting the growth rate. On the other hand, the conserved ftsK appeared to be essential in this bacterium. In conclusion, the canonical bacterial cell division machinery is not essential in P. limnophila and this bacterium divides via budding using an unknown mechanism.
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Affiliation(s)
- Elena Rivas-Marin
- Centro Andaluz de Biología del Desarrollo (CABD)-CSIC, Pablo de Olavide University, Seville, Spain
| | - Stijn H Peeters
- Department of Microbiology, IWWR, Faculty of Science, Radboud University, Nijmegen, The Netherlands
| | - Laura Claret Fernández
- Centro Andaluz de Biología del Desarrollo (CABD)-CSIC, Pablo de Olavide University, Seville, Spain.,Department of Microbiology, IWWR, Faculty of Science, Radboud University, Nijmegen, The Netherlands
| | - Christian Jogler
- Department of Microbiology, IWWR, Faculty of Science, Radboud University, Nijmegen, The Netherlands.,Institute of Microbiology, Department of Microbial Interactions, Friedrich-Schiller-Universität Jena, Jena, Germany
| | - Laura van Niftrik
- Department of Microbiology, IWWR, Faculty of Science, Radboud University, Nijmegen, The Netherlands
| | - Sandra Wiegand
- Department of Microbiology, IWWR, Faculty of Science, Radboud University, Nijmegen, The Netherlands
| | - Damien P Devos
- Centro Andaluz de Biología del Desarrollo (CABD)-CSIC, Pablo de Olavide University, Seville, Spain.
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13
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Dethlefsen S, Jäger C, Klockgether J, Schomburg D, Tümmler B. Metabolite profiling of the cold adaptation of Pseudomonas putida KT2440 and cold-sensitive mutants. ENVIRONMENTAL MICROBIOLOGY REPORTS 2019; 11:777-783. [PMID: 31503400 DOI: 10.1111/1758-2229.12793] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 09/02/2019] [Accepted: 09/08/2019] [Indexed: 06/10/2023]
Abstract
Free-living bacteria such as Pseudomonas putida are frequently exposed to temperature shifts and non-optimal growth conditions. We compared the transcriptome and metabolome of the cold adaptation of P. putida KT2440 and isogenic cold-sensitive transposon mutants carrying transposons in their cbrA, cbrB, pcnB, vacB, and bipA genes. Pseudomonas putida changes the mRNA expression of about 43% of all annotated open reading frames during this initial phase of cold adaptation, but only a small number of 6-93 genes were differentially expressed at 10°C between the wild-type strain and the individual mutants. The spectrum of metabolites underwent major changes during cold adaptation particularly in the mutants. Both the KT2440 strain and the mutants increased the levels of the most abundant sugars and amino acids which were more pronounced in the cold-sensitive mutants. All mutants depleted their pools for core metabolites of aromatic and sugar metabolism, but increased their pool of polar amino acids which should be advantageous to cope with the cold stress.
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Affiliation(s)
- Sarah Dethlefsen
- Molecular Pathology of Cystic Fibrosis and Pseudomonas Genomics, Clinical Research Group, Hannover Medical School, 30625, Hannover, Germany
| | - Christian Jäger
- Department of Biochemistry and Bioinformatics, Institute for Biochemistry and Biotechnology, Technische Universität Braunschweig, 38106, Braunschweig, Germany
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Jens Klockgether
- Molecular Pathology of Cystic Fibrosis and Pseudomonas Genomics, Clinical Research Group, Hannover Medical School, 30625, Hannover, Germany
| | - Dietmar Schomburg
- Department of Biochemistry and Bioinformatics, Institute for Biochemistry and Biotechnology, Technische Universität Braunschweig, 38106, Braunschweig, Germany
| | - Burkhard Tümmler
- Molecular Pathology of Cystic Fibrosis and Pseudomonas Genomics, Clinical Research Group, Hannover Medical School, 30625, Hannover, Germany
- Clinic for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, 30625, Hannover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), German Center for Lung Research, Hannover, Germany
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14
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Monteagudo-Cascales E, García-Mauriño SM, Santero E, Canosa I. Unraveling the role of the CbrA histidine kinase in the signal transduction of the CbrAB two-component system in Pseudomonas putida. Sci Rep 2019; 9:9110. [PMID: 31235731 PMCID: PMC6591292 DOI: 10.1038/s41598-019-45554-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 06/10/2019] [Indexed: 12/24/2022] Open
Abstract
The histidine kinase CbrA of the CbrAB two-component system of Pseudomonas putida is a key element to recognise the activating signal and mediate auto- and trans-phosphorylation of the response element CbrB. CbrA is encoded by the gene cbrA which is located downstream of a putative open reading frame we have named cbrX. We describe the role of the CbrX product in the expression of CbrA and show there is translational coupling of the genes. We also explore the role of the transmembrane (TM) and PAS domains of CbrA in the signal recognition. A ΔcbrXA mutant lacking its TM domains is uncoupled in its growth in histidine and citrate as carbon sources, but its overexpression restores the ability to grow in such carbon sources. In these conditions ΔTM-CbrA is able to respond to carbon availability, thus suggesting an intracellular nature for the signal sensed.
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Affiliation(s)
- Elizabet Monteagudo-Cascales
- Universidad Pablo de Olavide, Centro Andaluz de Biología del Desarrollo/Consejo Superior de Investigaciones Científicas/Junta de Andalucía, Seville, Spain
| | - Sofía M García-Mauriño
- Universidad Pablo de Olavide, Centro Andaluz de Biología del Desarrollo/Consejo Superior de Investigaciones Científicas/Junta de Andalucía, Seville, Spain
| | - Eduardo Santero
- Universidad Pablo de Olavide, Centro Andaluz de Biología del Desarrollo/Consejo Superior de Investigaciones Científicas/Junta de Andalucía, Seville, Spain
| | - Inés Canosa
- Universidad Pablo de Olavide, Centro Andaluz de Biología del Desarrollo/Consejo Superior de Investigaciones Científicas/Junta de Andalucía, Seville, Spain.
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15
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González-Flores YE, de Dios R, Reyes-Ramírez F, Santero E. The response of Sphingopyxis granuli strain TFA to the hostile anoxic condition. Sci Rep 2019; 9:6297. [PMID: 31000749 PMCID: PMC6472365 DOI: 10.1038/s41598-019-42768-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 04/05/2019] [Indexed: 01/02/2023] Open
Abstract
Sphingomonads comprises a group of interesting aerobic bacteria because of their ubiquity and metabolic capability of degrading many recalcitrant contaminants. The tetralin-degrader Sphingopyxis granuli strain TFA has been recently reported as able to anaerobically grow using nitrate as the alternative electron acceptor and so far is the only bacterium with this ability within the sphingomonads group. To understand how strain TFA thrives under anoxic conditions, a differential transcriptomic analysis while growing under aerobic or anoxic conditions was performed. This analysis has been validated and complemented with transcription kinetics of representative genes of different functional categories. Results show an extensive change of the expression pattern of this strain in the different conditions. Consistently, the most induced operon in anoxia codes for proteases, presumably required for extensive changes in the protein profile. Besides genes that respond to lack of oxygen in other bacteria, there are a number of genes that respond to stress or to damage of macromolecules, including genes of the SOS DNA-damage response, which suggest that anoxic conditions represent a hostile environment for this bacterium. Interestingly, growth under anoxic conditions also resulted in repression of all flagellar and type IV pilin genes, which suggested that this strain shaves its appendages off while growing in anaerobiosis.
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Affiliation(s)
- Yolanda Elisabet González-Flores
- Centro Andaluz de Biología del Desarrollo/CSIC/Universidad Pablo de Olavide/Junta de Andalucía. Departamento de Biología Molecular e Ingeniería Bioquímica, Seville, Spain
| | - Rubén de Dios
- Centro Andaluz de Biología del Desarrollo/CSIC/Universidad Pablo de Olavide/Junta de Andalucía. Departamento de Biología Molecular e Ingeniería Bioquímica, Seville, Spain
| | - Francisca Reyes-Ramírez
- Centro Andaluz de Biología del Desarrollo/CSIC/Universidad Pablo de Olavide/Junta de Andalucía. Departamento de Biología Molecular e Ingeniería Bioquímica, Seville, Spain.
| | - Eduardo Santero
- Centro Andaluz de Biología del Desarrollo/CSIC/Universidad Pablo de Olavide/Junta de Andalucía. Departamento de Biología Molecular e Ingeniería Bioquímica, Seville, Spain
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16
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Hueso-Gil Á, Calles B, O'Toole GA, de Lorenzo V. Gross transcriptomic analysis of Pseudomonas putida for diagnosing environmental shifts. Microb Biotechnol 2019; 13:263-273. [PMID: 30957409 PMCID: PMC6922523 DOI: 10.1111/1751-7915.13404] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 03/10/2019] [Accepted: 03/12/2019] [Indexed: 01/24/2023] Open
Abstract
The biological regime of Pseudomonas putida (and any other bacterium) under given environmental conditions results from the hierarchical expression of sets of genes that become turned on and off in response to one or more physicochemical signals. In some cases, such signals are clearly defined, but in many others, cells are exposed to a whole variety of ill-defined inputs that occur simultaneously. Transcriptomic analyses of bacteria passed from a reference condition to a complex niche can thus expose both the type of signals that they experience during the transition and the functions involved in adaptation to the new scenario. In this article, we describe a complete protocol for generation of transcriptomes aimed at monitoring the physiological shift of P. putida between two divergent settings using as a simple case study the change between homogeneous, planktonic lifestyle in a liquid medium and growth on the surface of an agar plate. To this end, RNA was collected from P. putidaKT2440 cells at various times after growth in either condition, and the genome-wide transcriptional outputs were analysed. While the role of individual genes needs to be verified on a case-by-case basis, a gross inspection of the resulting profiles suggested cells that are cultured on solid media consistently had a higher translational and metabolic activity, stopped production of flagella and were conspicuously exposed to a strong oxidative stress. The herein described methodology is generally applicable to other circumstances for diagnosing lifestyle determinants of interest.
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Affiliation(s)
- Ángeles Hueso-Gil
- Systems Biology Program, Centro Nacional de Biotecnología-CSIC, Campus de Cantoblanco, Madrid, 28049, Spain
| | - Belén Calles
- Systems Biology Program, Centro Nacional de Biotecnología-CSIC, Campus de Cantoblanco, Madrid, 28049, Spain
| | - George A O'Toole
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, 03755, USA
| | - Víctor de Lorenzo
- Systems Biology Program, Centro Nacional de Biotecnología-CSIC, Campus de Cantoblanco, Madrid, 28049, Spain
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17
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Barroso R, García-Mauriño SM, Tomás-Gallardo L, Andújar E, Pérez-Alegre M, Santero E, Canosa I. The CbrB Regulon: Promoter dissection reveals novel insights into the CbrAB expression network in Pseudomonas putida. PLoS One 2018; 13:e0209191. [PMID: 30557364 PMCID: PMC6296734 DOI: 10.1371/journal.pone.0209191] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 11/30/2018] [Indexed: 11/18/2022] Open
Abstract
CbrAB is a high ranked global regulatory system exclusive of the Pseudomonads that responds to carbon limiting conditions. It has become necessary to define the particular regulon of CbrB and discriminate it from the downstream cascades through other regulatory components. We have performed in vivo binding analysis of CbrB in P. putida and determined that it directly controls the expression of at least 61 genes; 20% involved in regulatory functions, including the previously identified CrcZ and CrcY small regulatory RNAs. The remaining are porines or transporters (20%), metabolic enzymes (16%), activities related to protein translation (5%) and orfs of uncharacterised function (38%). Amongst the later, we have selected the operon PP2810-13 to make an exhaustive analysis of the CbrB binding sequences, together with those of crcZ and crcY. We describe the implication of three independent non-palindromic subsites with a variable spacing in three different targets; CrcZ, CrcY and operon PP2810-13 in the CbrAB activation. CbrB is a quite peculiar σN-dependent activator since it is barely dependent on phosphorylation for transcriptional activation. With the depiction of the precise contacts of CbrB with the DNA, the analysis of the multimerisation status and its dependence on other factors such as RpoN o IHF, we propose a model of transcriptional activation.
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Affiliation(s)
- Rocío Barroso
- Universidad Pablo de Olavide, Centro Andaluz de Biología del Desarrollo/ Consejo Superior de Investigaciones Científicas/ Junta de Andalucía, Seville, Spain
| | - Sofía M. García-Mauriño
- Universidad Pablo de Olavide, Centro Andaluz de Biología del Desarrollo/ Consejo Superior de Investigaciones Científicas/ Junta de Andalucía, Seville, Spain
| | | | - Eloísa Andújar
- Genomics unit, CABIMER/ CSIC/ Universidad de Sevilla/ Universidad Pablo de Olavide/ Junta de Andalucía, Seville, Spain
| | - Mónica Pérez-Alegre
- Genomics unit, CABIMER/ CSIC/ Universidad de Sevilla/ Universidad Pablo de Olavide/ Junta de Andalucía, Seville, Spain
| | - Eduardo Santero
- Universidad Pablo de Olavide, Centro Andaluz de Biología del Desarrollo/ Consejo Superior de Investigaciones Científicas/ Junta de Andalucía, Seville, Spain
| | - Inés Canosa
- Universidad Pablo de Olavide, Centro Andaluz de Biología del Desarrollo/ Consejo Superior de Investigaciones Científicas/ Junta de Andalucía, Seville, Spain
- * E-mail:
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18
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García-Romero I, Förstner KU, Santero E, Floriano B. SuhB, a small non-coding RNA involved in catabolite repression of tetralin degradation genes in Sphingopyxis granuli strain TFA. Environ Microbiol 2018; 20:3671-3683. [PMID: 30033661 DOI: 10.1111/1462-2920.14360] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 07/05/2018] [Accepted: 07/10/2018] [Indexed: 01/13/2023]
Abstract
Global dRNA-seq analysis of transcription start sites combined with in silico annotation using Infernal software revealed the expression of 91 putative non-coding sRNA in Sphingopyxis granuli TFA cells grown on different carbon sources. Excluding housekeeping sRNAs, only one additional sRNA, which belongs to the Rfam SuhB family (RF00519), was detected by Infernal but with an incorrect size according to the experimental results. SuhB is highly conserved across the Sphingopyxis genus. Expression data revealed that SuhB is present in rapidly growing TFA cells. A suhB deletion mutant exhibited de-repression of tetralin degradation (thn) gene expression and higher amounts of their LysR-type activator, ThnR, under conditions of carbon catabolite repression (CCR). Interaction between SuhB and the 5'UTR of thnR mRNA was demonstrated in vitro. Moreover, co-immunoprecipitation experiments, combined with fluorescence measurements of gfp fusions to the 5'UTR of thnR mRNA and the phenotype of an hfq deletion mutant, suggest the involvement of Hfq in this interaction. Taken together, these data support an Hfq-mediated repressive role for SuhB, on ThnR mRNA translation that prevents thn gene induction. SuhB, which is a highly conserved sRNA in the Sphingopyxis genus, is the first identified element directly involved in CCR of thn gene expression in S. granuli strain TFA.
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Affiliation(s)
| | - Konrad U Förstner
- Research Center for Infectious Diseases (ZINF), University of Würzburg, 97080, Würzburg, Germany
| | - Eduardo Santero
- Centro Andaluz de Biología del Desarrollo, CSIC-Universidad Pablo de Olavide, Seville, Spain
| | - Belén Floriano
- Centro Andaluz de Biología del Desarrollo, CSIC-Universidad Pablo de Olavide, Seville, Spain
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19
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Sánchez-Hevia DL, Yuste L, Moreno R, Rojo F. Influence of the Hfq and Crc global regulators on the control of iron homeostasis inPseudomonas putida. Environ Microbiol 2018; 20:3484-3503. [DOI: 10.1111/1462-2920.14263] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 04/27/2018] [Accepted: 04/27/2018] [Indexed: 01/01/2023]
Affiliation(s)
- Dione L. Sánchez-Hevia
- Departamento de Biotecnología Microbiana; Centro Nacional de Biotecnología, CSIC, Darwin 3, Cantoblanco; Madrid, 28049 Spain
| | - Luis Yuste
- Departamento de Biotecnología Microbiana; Centro Nacional de Biotecnología, CSIC, Darwin 3, Cantoblanco; Madrid, 28049 Spain
| | - Renata Moreno
- Departamento de Biotecnología Microbiana; Centro Nacional de Biotecnología, CSIC, Darwin 3, Cantoblanco; Madrid, 28049 Spain
| | - Fernando Rojo
- Departamento de Biotecnología Microbiana; Centro Nacional de Biotecnología, CSIC, Darwin 3, Cantoblanco; Madrid, 28049 Spain
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20
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Thuptimdang P, Limpiyakorn T, Khan E. Dependence of toxicity of silver nanoparticles on Pseudomonas putida biofilm structure. CHEMOSPHERE 2017; 188:199-207. [PMID: 28886554 DOI: 10.1016/j.chemosphere.2017.08.147] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Revised: 08/27/2017] [Accepted: 08/28/2017] [Indexed: 06/07/2023]
Abstract
Susceptibility of biofilms with different physical structures to silver nanoparticles (AgNPs) was studied. Biofilms of Pseudomonas putida KT2440 were formed in batch conditions under different carbon sources (glucose, glutamic acid, and citrate), glucose concentrations (5 and 50 mM), and incubation temperatures (25 and 30 °C). The biofilms were observed using confocal laser scanning microscopy for their physical characteristics (biomass amount, thickness, biomass volume, surface to volume ratio, and roughness coefficient). The biofilms forming under different growth conditions exhibited different physical structures. The biofilm thickness and the roughness coefficient were found negatively and positively correlated with the biofilm susceptibility to AgNPs, respectively. The effect of AgNPs on biofilms was low (1-log reduction of cell number) when the biofilms had high biomass amount, high thickness, high biomass volume, low surface to volume ratio, and low roughness coefficient. Furthermore, the extracellular polymeric substance (EPS) stripping process was applied to confirm the dependence of susceptibility to AgNPs on the structure of biofilm. After the EPS stripping process, the biofilms forming under different conditions showed reduction in thickness and biomass volume, and increases in surface to volume ratio and roughness coefficient, which led to more biofilm susceptibility to AgNPs. The results of this study suggest that controlling the growth conditions to alter the biofilm physical structure is a possible approach to reduce the impact of AgNPs on biofilms in engineered and natural systems.
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Affiliation(s)
- Pumis Thuptimdang
- International Program in Hazardous Substance and Environmental Management, Graduate School, Chulalongkorn University, Bangkok, 10330, Thailand; Center of Excellence on Hazardous Substance Management (HSM), Bangkok, 10330, Thailand.
| | - Tawan Limpiyakorn
- Department of Environmental Engineering, Chulalongkorn University, Bangkok, 10330, Thailand; Research Program in Hazardous Substance Management in Agricultural Industry, Center of Excellence on Hazardous Substance Management (HSM), Bangkok, 10330, Thailand; Research Unit Control of Emerging Micropollutants in Environment, Chulalongkorn University, Bangkok, 10330, Thailand.
| | - Eakalak Khan
- Department of Civil and Environmental Engineering, North Dakota State University, Fargo, ND, 58108, USA.
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21
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Ainelo H, Lahesaare A, Teppo A, Kivisaar M, Teras R. The promoter region of lapA and its transcriptional regulation by Fis in Pseudomonas putida. PLoS One 2017; 12:e0185482. [PMID: 28945818 PMCID: PMC5612765 DOI: 10.1371/journal.pone.0185482] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 09/13/2017] [Indexed: 12/28/2022] Open
Abstract
LapA is the biggest protein in Pseudomonas putida and a key factor for biofilm formation. Its importance and posttranslational regulation is rather thoroughly studied but less is known about the transcriptional regulation. Here we give evidence that transcription of lapA in LB-grown bacteria is initiated from six promoters, three of which display moderate RpoS-dependence. The global transcription regulator Fis binds to the lapA promoter area at six positions in vitro, and Fis activates the transcription of lapA while overexpressed in cells. Two of the six Fis binding sites, Fis-A7 and Fis-A5, are necessary for the positive effect of Fis on the transcription of lapA in vivo. Our results indicate that Fis binding to the Fis-A7 site increases the level of transcription from the most distal promoter of lapA, whereas Fis binding to the Fis-A5 site could be important for modifying the promoter area topology.
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Affiliation(s)
- Hanna Ainelo
- Chair of Genetics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Andrio Lahesaare
- Chair of Genetics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Annika Teppo
- Chair of Genetics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Maia Kivisaar
- Chair of Genetics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Riho Teras
- Chair of Genetics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
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22
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Sun Z, Vasileva D, Suzuki-Minakuchi C, Okada K, Luo F, Igarashi Y, Nojiri H. Growth phase-dependent expression profiles of three vital H-NS family proteins encoded on the chromosome of Pseudomonas putida KT2440 and on the pCAR1 plasmid. BMC Microbiol 2017; 17:188. [PMID: 28851281 PMCID: PMC5576294 DOI: 10.1186/s12866-017-1091-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 08/11/2017] [Indexed: 01/09/2023] Open
Abstract
Background H-NS family proteins are nucleoid-associated proteins that form oligomers on DNA and function as global regulators. They are found in both bacterial chromosomes and plasmids, and were suggested to be candidate effectors of the interaction between them. TurA and TurB are the predominantly expressed H-NS family proteins encoded on the chromosome of Pseudomonas putida KT2440, while Pmr is encoded on the carbazole-degradative incompatibility group P-7 plasmid pCAR1. Previous transcriptome analyses suggested that they function cooperatively, but play different roles in the global transcriptional network. In addition to differences in protein interaction and DNA-binding functions, cell expression levels are important in clarifying the detailed underlying mechanisms. Here, we determined the precise protein amounts of TurA, TurB, and Pmr in KT2440 in the presence and absence of pCAR1. Results The intracellular amounts of TurA and TurB in KT2440 and KT2440(pCAR1) were determined by quantitative western blot analysis using specific antibodies. The amount of TurA decreased from the log phase (~80,000 monomers per cell) to the stationary phase (~20,000 monomers per cell), while TurB was only detectable upon entry into the stationary phase (maximum 6000 monomers per cell). Protein amounts were not affected by pCAR1 carriage. KT2440(pCAR1pmrHis), where histidine-tagged Pmr is expressed under its original promotor, was used to determine the intracellular amount of Pmr, which was constant (~30,000 monomers per cell) during cell growth. Quantitative reverse transcription PCR demonstrated that the transcriptional levels of turA and turB were consistent with protein expression, though the transcriptional and translational profiles of Pmr differed. Conclusion The amount of TurB increases as TurA decreases, and the amount of Pmr does not affect the amounts of TurA and TurB. This is consistent with our previous observation that TurA and TurB play complementary roles, whereas Pmr works relatively independently. This study provides insight into the molecular mechanisms underlying reconstitution of the transcriptional network in KT2440 by pCAR1 carriage. Electronic supplementary material The online version of this article (doi:10.1186/s12866-017-1091-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zongping Sun
- Research Center of Bioenergy & Bioremediation, College of Resources and Environment, Southwest University, No.2 Tiansheng Road, BeiBei District, Chongqing, 400715, China.,Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Delyana Vasileva
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Chiho Suzuki-Minakuchi
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Kazunori Okada
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Feng Luo
- Research Center of Bioenergy & Bioremediation, College of Resources and Environment, Southwest University, No.2 Tiansheng Road, BeiBei District, Chongqing, 400715, China
| | - Yasuo Igarashi
- Research Center of Bioenergy & Bioremediation, College of Resources and Environment, Southwest University, No.2 Tiansheng Road, BeiBei District, Chongqing, 400715, China
| | - Hideaki Nojiri
- Research Center of Bioenergy & Bioremediation, College of Resources and Environment, Southwest University, No.2 Tiansheng Road, BeiBei District, Chongqing, 400715, China. .,Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.
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23
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Poblete-Castro I, Borrero-de Acuña JM, Nikel PI, Kohlstedt M, Wittmann C. Host Organism: Pseudomonas putida. Ind Biotechnol (New Rochelle N Y) 2016. [DOI: 10.1002/9783527807796.ch8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Ignacio Poblete-Castro
- Universidad Andrés Bello; Center for Bioinformatics and Integrative Biology, Biosystems Engineering Laboratory, Faculty of Biological Sciences; Av. República 239 8340176 Santiago de Chile Chile
| | - José M. Borrero-de Acuña
- Universidad Andrés Bello; Center for Bioinformatics and Integrative Biology, Biosystems Engineering Laboratory, Faculty of Biological Sciences; Av. República 239 8340176 Santiago de Chile Chile
| | - Pablo I. Nikel
- Systems and Synthetic Biology Program; National Spanish Center for Biotechnology (CNB-CSIC); Calle Darwin, 3 28049 Madrid, Spain
| | - Michael Kohlstedt
- Saarland University; Institute of Systems Biology, Biosciences; Campus A1.5 66123 Saarbrücken, Germany
| | - Christoph Wittmann
- Saarland University; Institute of Systems Biology, Biosciences; Campus A1.5 66123 Saarbrücken, Germany
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24
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Suzuki-Minakuchi C, Kawazuma K, Matsuzawa J, Vasileva D, Fujimoto Z, Terada T, Okada K, Nojiri H. Structural similarities and differences in H-NS family proteins revealed by the N-terminal structure of TurB in Pseudomonas putida KT2440. FEBS Lett 2016; 590:3583-3594. [PMID: 27709616 DOI: 10.1002/1873-3468.12425] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 09/12/2016] [Accepted: 09/14/2016] [Indexed: 11/08/2022]
Abstract
H-NS family proteins play key roles in bacterial nucleoid compaction and global transcription. MvaT homologues in Pseudomonas have almost negligible amino acid sequence identity with H-NS, but can complement an hns-related phenotype of Escherichia coli. Here, we report the crystal structure of the N-terminal dimerization/oligomerization domain of TurB, an MvaT homologue in Pseudomonas putida KT2440. Our data identify two dimerization sites; the structure of the central dimerization site is almost the same as the corresponding region of H-NS, whereas the terminal dimerization sites are different. Our results reveal similarities and differences in dimerization and oligomerization mechanisms between H-NS and TurB.
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Affiliation(s)
| | - Kohei Kawazuma
- Biotechnology Research Center, The University of Tokyo, Japan
| | - Jun Matsuzawa
- Biotechnology Research Center, The University of Tokyo, Japan
| | | | - Zui Fujimoto
- Advanced Analysis Center, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Tohru Terada
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Japan.,Agricultural Bioinformatics Research Unit, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Japan
| | - Kazunori Okada
- Biotechnology Research Center, The University of Tokyo, Japan
| | - Hideaki Nojiri
- Biotechnology Research Center, The University of Tokyo, Japan. .,Agricultural Bioinformatics Research Unit, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Japan.
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Quesada JM, Fernández M, Soriano MI, Barrientos-Moreno L, Llamas MA, Espinosa-Urgel M. Rhizosphere selection of Pseudomonas putida KT2440 variants with increased fitness associated to changes in gene expression. ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:842-850. [PMID: 27487165 DOI: 10.1111/1758-2229.12447] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
As the interface between plant roots and soil, the rhizosphere is a complex environment where nutrients released by the plant promote microbial growth. Increasing evidences indicate that the plant also exerts a selective pressure on microbial populations in the rhizosphere, favouring colonization by certain groups. In this work, we have designed an experimental setup to begin analysing the evolution of a specific bacterial population in the rhizosphere, using Pseudomonas putida KT2440 as model organism. After several rounds of selection without passage through laboratory growth conditions, derivatives of this strain with increased fitness in the rhizosphere were isolated. Detailed analysis of one of these clones indicated that this effect is specific for rhizosphere conditions and derives from changes in its transcriptional profile in this environment, with 43 genes being differentially expressed with respect to the parental strain. Several of these genes belong to functional categories which could affect stress adaptation and availability of particular nutrients. By inactivating two genes identified as upregulated in the selected clone (coding for a stress-response protein and a rRNA modifying protein), these functions were shown to contribute to rhizosphere fitness. Our data also suggest the existence of different evolutionary pathways leading to increased rhizosphere fitness.
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Affiliation(s)
- José Miguel Quesada
- Departamento de Protección Ambiental, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Profesor Albareda 1, Granada, E-18008, Spain
| | - Matilde Fernández
- Departamento de Protección Ambiental, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Profesor Albareda 1, Granada, E-18008, Spain
| | - María Isabel Soriano
- Departamento de Protección Ambiental, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Profesor Albareda 1, Granada, E-18008, Spain
| | - Laura Barrientos-Moreno
- Departamento de Protección Ambiental, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Profesor Albareda 1, Granada, E-18008, Spain
| | - María Antonia Llamas
- Departamento de Protección Ambiental, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Profesor Albareda 1, Granada, E-18008, Spain
| | - Manuel Espinosa-Urgel
- Departamento de Protección Ambiental, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Profesor Albareda 1, Granada, E-18008, Spain
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Jiménez-Fernández A, López-Sánchez A, Jiménez-Díaz L, Navarrete B, Calero P, Platero AI, Govantes F. Complex Interplay between FleQ, Cyclic Diguanylate and Multiple σ Factors Coordinately Regulates Flagellar Motility and Biofilm Development in Pseudomonas putida. PLoS One 2016; 11:e0163142. [PMID: 27636892 PMCID: PMC5026340 DOI: 10.1371/journal.pone.0163142] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Accepted: 09/02/2016] [Indexed: 01/01/2023] Open
Abstract
Most bacteria alternate between a free living planktonic lifestyle and the formation of structured surface-associated communities named biofilms. The transition between these two lifestyles requires a precise and timely regulation of the factors involved in each of the stages that has been likened to a developmental process. Here we characterize the involvement of the transcriptional regulator FleQ and the second messenger cyclic diguanylate in the coordinate regulation of multiple functions related to motility and surface colonization in Pseudomonas putida. Disruption of fleQ caused strong defects in flagellar motility, biofilm formation and surface attachment, and the ability of this mutation to suppress multiple biofilm-related phenotypes associated to cyclic diguanylate overproduction suggests that FleQ mediates cyclic diguanylate signaling critical to biofilm growth. We have constructed a library containing 94 promoters potentially involved in motility and biofilm development fused to gfp and lacZ, screened this library for FleQ and cyclic diguanylate regulation, and assessed the involvement of alternative σ factors σN and FliA in the transcription of FleQ-regulated promoters. Our results suggest a dual mode of action for FleQ. Low cyclic diguanylate levels favor FleQ interaction with σN-dependent promoters to activate the flagellar cascade, encompassing the flagellar cluster and additional genes involved in cyclic diguanylate metabolism, signal transduction and gene regulation. On the other hand, characterization of the FleQ-regulated σN- and FliA-independent PlapA and PbcsD promoters revealed two disparate regulatory mechanisms leading to a similar outcome: the synthesis of biofilm matrix components in response to increased cyclic diguanylate levels.
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Affiliation(s)
- Alicia Jiménez-Fernández
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide/Consejo Superior de Investigaciones Científicas/Junta de Andalucía, Sevilla, Spain; and Departamento de Biología Molecular e Ingeniería Bioquímica, Universidad Pablo de Olavide, Carretera de Utrera, Km. 1, 41013, Sevilla, Spain
| | - Aroa López-Sánchez
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide/Consejo Superior de Investigaciones Científicas/Junta de Andalucía, Sevilla, Spain; and Departamento de Biología Molecular e Ingeniería Bioquímica, Universidad Pablo de Olavide, Carretera de Utrera, Km. 1, 41013, Sevilla, Spain
| | - Lorena Jiménez-Díaz
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide/Consejo Superior de Investigaciones Científicas/Junta de Andalucía, Sevilla, Spain; and Departamento de Biología Molecular e Ingeniería Bioquímica, Universidad Pablo de Olavide, Carretera de Utrera, Km. 1, 41013, Sevilla, Spain
| | - Blanca Navarrete
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide/Consejo Superior de Investigaciones Científicas/Junta de Andalucía, Sevilla, Spain; and Departamento de Biología Molecular e Ingeniería Bioquímica, Universidad Pablo de Olavide, Carretera de Utrera, Km. 1, 41013, Sevilla, Spain
| | - Patricia Calero
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide/Consejo Superior de Investigaciones Científicas/Junta de Andalucía, Sevilla, Spain; and Departamento de Biología Molecular e Ingeniería Bioquímica, Universidad Pablo de Olavide, Carretera de Utrera, Km. 1, 41013, Sevilla, Spain
| | - Ana Isabel Platero
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide/Consejo Superior de Investigaciones Científicas/Junta de Andalucía, Sevilla, Spain; and Departamento de Biología Molecular e Ingeniería Bioquímica, Universidad Pablo de Olavide, Carretera de Utrera, Km. 1, 41013, Sevilla, Spain
| | - Fernando Govantes
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide/Consejo Superior de Investigaciones Científicas/Junta de Andalucía, Sevilla, Spain; and Departamento de Biología Molecular e Ingeniería Bioquímica, Universidad Pablo de Olavide, Carretera de Utrera, Km. 1, 41013, Sevilla, Spain
- * E-mail:
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Glutathione-Disrupted Biofilms of Clinical Pseudomonas aeruginosa Strains Exhibit an Enhanced Antibiotic Effect and a Novel Biofilm Transcriptome. Antimicrob Agents Chemother 2016; 60:4539-51. [PMID: 27161630 DOI: 10.1128/aac.02919-15] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 05/04/2016] [Indexed: 11/20/2022] Open
Abstract
Pseudomonas aeruginosa infections result in high morbidity and mortality rates for individuals with cystic fibrosis (CF), with premature death often occurring. These infections are complicated by the formation of biofilms in the sputum. Antibiotic therapy is stymied by antibiotic resistance of the biofilm matrix, making novel antibiofilm strategies highly desirable. Within P. aeruginosa biofilms, the redox factor pyocyanin enhances biofilm integrity by intercalating with extracellular DNA. The antioxidant glutathione (GSH) reacts with pyocyanin, disrupting intercalation. This study investigated GSH disruption by assaying the physiological effects of GSH and DNase I on biofilms of clinical CF isolates grown in CF artificial sputum medium (ASMDM+). Confocal scanning laser microscopy showed that 2 mM GSH, alone or combined with DNase I, significantly disrupted immature (24-h) biofilms of Australian epidemic strain (AES) isogens AES-1R and AES-1M. GSH alone greatly disrupted mature (72-h) AES-1R biofilms, resulting in significant differential expression of 587 genes, as indicated by RNA-sequencing (RNA-seq) analysis. Upregulated systems included cyclic diguanylate and pyoverdine biosynthesis, the type VI secretion system, nitrate metabolism, and translational machinery. Biofilm disruption with GSH revealed a cellular physiology distinct from those of mature and dispersed biofilms. RNA-seq results were validated by biochemical and quantitative PCR assays. Biofilms of a range of CF isolates disrupted with GSH and DNase I were significantly more susceptible to ciprofloxacin, and increased antibiotic effectiveness was achieved by increasing the GSH concentration. This study demonstrated that GSH, alone or with DNase I, represents an effective antibiofilm treatment when combined with appropriate antibiotics, pending in vivo studies.
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Chaithawiwat K, Vangnai A, McEvoy JM, Pruess B, Krajangpan S, Khan E. Impact of nanoscale zero valent iron on bacteria is growth phase dependent. CHEMOSPHERE 2016; 144:352-9. [PMID: 26378872 DOI: 10.1016/j.chemosphere.2015.09.025] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Revised: 08/31/2015] [Accepted: 09/06/2015] [Indexed: 05/20/2023]
Abstract
The toxic effect of nanoscale zero valent iron (nZVI) particles on bacteria from different growth phases was studied. Four bacterial strains namely Escherichia coli strains JM109 and BW25113, and Pseudomonas putida strains KT2440 and F1 were experimented. The growth curves of these strains were determined. Bacterial cells were harvested based on the predetermined time points, and exposed to nZVI. Cell viability was determined by the plate count method. Bacterial cells in lag and stationary phases showed higher resistance to nZVI for all four bacterial strains, whereas cells in exponential and decline phases were less resistant to nZVI and were rapidly inactivated when exposed to nZVI. Bacterial inactivation increased with the concentration of nZVI. Furthermore, less than 14% bacterial inactivation was observed when bacterial cells were exposed to the filtrate of nZVI suspension suggesting that the physical interaction between nZVI and cell is necessary for bacterial inactivation.
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Affiliation(s)
- Krittanut Chaithawiwat
- International Postgraduate Programs in Environmental Management, Graduate School Chulalongkorn University, Bangkok 10330, Thailand; Environmental and Conservation Sciences, North Dakota State University, Fargo, ND 58108, USA
| | - Alisa Vangnai
- Department of Biochemistry, Chulalongkorn University, Bangkok 10330, Thailand
| | - John M McEvoy
- Department of Veterinary and Microbiological Sciences, North Dakota State University, Fargo, ND 58108, USA
| | - Birgit Pruess
- Department of Veterinary and Microbiological Sciences, North Dakota State University, Fargo, ND 58108, USA
| | | | - Eakalak Khan
- Department of Civil and Environmental Engineering, North Dakota State University, Fargo, ND 58108, USA.
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29
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Mohareb F, Iriondo M, Doulgeraki AI, Van Hoek A, Aarts H, Cauchi M, Nychas GJE. Identification of meat spoilage gene biomarkers in Pseudomonas putida using gene profiling. Food Control 2015. [DOI: 10.1016/j.foodcont.2015.04.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Lahesaare A, Moor H, Kivisaar M, Teras R. Pseudomonas putida Fis binds to the lapF promoter in vitro and represses the expression of LapF. PLoS One 2014; 9:e115901. [PMID: 25545773 PMCID: PMC4278767 DOI: 10.1371/journal.pone.0115901] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 12/02/2014] [Indexed: 11/19/2022] Open
Abstract
The biofilm matrix of the rhizospheric bacterium Pseudomonas putida consists mainly of a proteinaceous component. The two largest P. putida proteins, adhesins LapA and LapF, are involved in biofilm development but prevail in different developmental stages of the biofilm matrix. LapA is abundant in the initial stage of biofilm formation whereas LapF is found in the mature biofilm. Although the transcriptional regulation of the adhesins is not exhaustively studied, some factors that can be involved in their regulation have been described. For example, RpoS, the major stress response sigma factor, activates, and Fis represses LapF expression. This study focused on the LapF expression control by Fis. Indeed, using DNase I footprint analysis a Fis binding site Fis-F2 was located 150 bp upstream of the lapF gene coding sequence. The mapped 5' end of the lapF mRNA localized the promoter to the same region, overlapping with the Fis binding site Fis-F2. Monitoring the lapF promoter activity by a β-galactosidase assay revealed that Fis overexpression causes a 4-fold decrease in the transcriptional activity. Furthermore, mutations that diminished Fis binding to the Fis-F2 site abolished the repression of the lapF promoter. Thus, these data suggest that Fis is involved in the biofilm regulation via repression of LapF expression.
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Affiliation(s)
- Andrio Lahesaare
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Hanna Moor
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Maia Kivisaar
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Riho Teras
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
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31
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Wang Y, Lv M, Zhang Y, Xiao X, Jiang T, Zhang W, Hu C, Gao C, Ma C, Xu P. Reconstruction of lactate utilization system in Pseudomonas putida KT2440: a novel biocatalyst for l-2-hydroxy-carboxylate production. Sci Rep 2014; 4:6939. [PMID: 25373400 PMCID: PMC4221787 DOI: 10.1038/srep06939] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Accepted: 10/20/2014] [Indexed: 11/09/2022] Open
Abstract
As an important method for building blocks synthesis, whole cell biocatalysis is hindered by some shortcomings such as unpredictability of reactions, utilization of opportunistic pathogen, and side reactions. Due to its biological and extensively studied genetic background, Pseudomonas putida KT2440 is viewed as a promising host for construction of efficient biocatalysts. After analysis and reconstruction of the lactate utilization system in the P. putida strain, a novel biocatalyst that only exhibited NAD-independent D-lactate dehydrogenase activity was prepared and used in L-2-hydroxy-carboxylates production. Since the side reaction catalyzed by the NAD-independent L-lactate dehydrogenase was eliminated in whole cells of recombinant P. putida KT2440, two important L-2-hydroxy-carboxylates (L-lactate and L-2-hydroxybutyrate) were produced in high yield and high optical purity by kinetic resolution of racemic 2-hydroxy carboxylic acids. The results highlight the promise in biocatalysis by the biotechnologically important organism P. putida KT2440 through genomic analysis and recombination.
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Affiliation(s)
- Yujiao Wang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, People's Republic of China
| | - Min Lv
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, People's Republic of China
| | - Yingxin Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, People's Republic of China
| | - Xieyue Xiao
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, People's Republic of China
| | - Tianyi Jiang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, People's Republic of China
| | - Wen Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, People's Republic of China
| | - Chunhui Hu
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, People's Republic of China
| | - Chao Gao
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, People's Republic of China
| | - Cuiqing Ma
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, People's Republic of China
| | - Ping Xu
- 1] State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, People's Republic of China [2] State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
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32
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Moor H, Teppo A, Lahesaare A, Kivisaar M, Teras R. Fis overexpression enhances Pseudomonas putida biofilm formation by regulating the ratio of LapA and LapF. MICROBIOLOGY-SGM 2014; 160:2681-2693. [PMID: 25253613 DOI: 10.1099/mic.0.082503-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Bacteria form biofilm as a response to a number of environmental signals that are mediated by global transcription regulators and alarmones. Here we report the involvement of the global transcription regulator Fis in Pseudomonas putida biofilm formation through regulation of lapA and lapF genes. The major component of P. putida biofilm is proteinaceous and two large adhesive proteins, LapA and LapF, are known to play a key role in its formation. We have previously shown that Fis overexpression enhances P. putida biofilm formation. In this study, we used mini-Tn5 transposon mutagenesis to select potential Fis-regulated genes involved in biofilm formation. A total of 90 % of the studied transposon mutants carried insertions in the lap genes. Since our experiments showed that Fis-enhanced biofilm is mostly proteinaceous, the amounts of LapA and LapF from P. putida cells lysates were quantified using SDS-PAGE. Fis overexpression increases the quantity of LapA 1.6 times and decreases the amount of LapF at least 4 times compared to the wild-type cells. The increased LapA expression caused by Fis overexpression was confirmed by FACS analysis measuring the amount of LapA-GFP fusion protein. Our results suggest that the profusion of LapA in the Fis-overexpressed cells causes enhanced biofilm formation in mature stages of P. putida biofilm and LapF has a minor role in P. putida biofilm formation.
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Affiliation(s)
- Hanna Moor
- Institute of Molecular and Cell Biology, University of Tartu, Riia 23, 51010 Tartu, Estonia
| | - Annika Teppo
- Institute of Molecular and Cell Biology, University of Tartu, Riia 23, 51010 Tartu, Estonia
| | - Andrio Lahesaare
- Institute of Molecular and Cell Biology, University of Tartu, Riia 23, 51010 Tartu, Estonia
| | - Maia Kivisaar
- Institute of Molecular and Cell Biology, University of Tartu, Riia 23, 51010 Tartu, Estonia
| | - Riho Teras
- Institute of Molecular and Cell Biology, University of Tartu, Riia 23, 51010 Tartu, Estonia
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Lieder S, Jahn M, Seifert J, von Bergen M, Müller S, Takors R. Subpopulation-proteomics reveal growth rate, but not cell cycling, as a major impact on protein composition in Pseudomonas putida KT2440. AMB Express 2014; 4:71. [PMID: 25401072 PMCID: PMC4230896 DOI: 10.1186/s13568-014-0071-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 08/18/2014] [Indexed: 12/14/2022] Open
Abstract
Population heterogeneity occurring in industrial microbial bioprocesses is regarded as a putative effector causing performance loss in large scale. While the existence of subpopulations is a commonly accepted fact, their appearance and impact on process performance still remains rather unclear. During cell cycling, distinct subpopulations differing in cell division state and DNA content appear which contribute individually to the efficiency of the bioprocess. To identify stressed or impaired subpopulations, we analyzed the interplay of growth rate, cell cycle and phenotypic profile of subpopulations by using flow cytometry and cell sorting in conjunction with mass spectrometry based global proteomics. Adjusting distinct growth rates in chemostats with the model strain Pseudomonas putida KT2440, cells were differentiated by DNA content reflecting different cell cycle stages. The proteome of separated subpopulations at given growth rates was found to be highly similar, while different growth rates caused major changes of the protein inventory with respect to e.g. carbon storage, motility, lipid metabolism and the translational machinery. In conclusion, cells in various cell cycle stages at the same growth rate were found to have similar to identical proteome profiles showing no significant population heterogeneity on the proteome level. In contrast, the growth rate clearly determines the protein composition and therefore the metabolic strategy of the cells.
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Affiliation(s)
- Sarah Lieder
- Institute for Biochemical Engineering, University of Stuttgart, Allmandring 31, Stuttgart, Germany
| | - Michael Jahn
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research—UFZ, Permoserstr. 15, Leipzig, 04318, Germany
| | - Jana Seifert
- Department of Proteomics, Helmholtz Centre for Environmental Research—UFZ, Permoserstr. 15, Leipzig, 04318, Germany
- Institute of Animal Nutrition, University of Hohenheim, Emil-Wolff-Straße 8 and 10, Stuttgart, 70599, Germany
| | - Martin von Bergen
- Department of Proteomics, Helmholtz Centre for Environmental Research—UFZ, Permoserstr. 15, Leipzig, 04318, Germany
- Department of Metabolomics, Helmholtz Centre for Environmental Research—UFZ, Permoserstr. 15, Leipzig, 04318, Germany
- Department of Biotechnology, Chemistry and Environmental Engineering, University of Aalborg, Sohngaardsholmsvej 49, Aalborg, 9000, Denmark
| | - Susann Müller
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research—UFZ, Permoserstr. 15, Leipzig, 04318, Germany
| | - Ralf Takors
- Institute for Biochemical Engineering, University of Stuttgart, Allmandring 31, Stuttgart, Germany
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Suzuki C, Kawazuma K, Horita S, Terada T, Tanokura M, Okada K, Yamane H, Nojiri H. Oligomerization mechanisms of an H-NS family protein, Pmr, encoded on the plasmid pCAR1 provide a molecular basis for functions of H-NS family members. PLoS One 2014; 9:e105656. [PMID: 25137042 PMCID: PMC4138198 DOI: 10.1371/journal.pone.0105656] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Accepted: 07/26/2014] [Indexed: 11/19/2022] Open
Abstract
Enterobacterial H-NS-like proteins and Pseudomonas MvaT-like proteins share low homology at the amino acid sequence level, but both can function as xenogeneic silencers and are included in the H-NS family of proteins. H-NS family members have dimerization/oligomerization and DNA-binding domains connected by a flexible linker and form large nucleoprotein complexes using both domains. Pmr, an MvaT-like protein encoded on the IncP-7 carbazole-degradative plasmid pCAR1, is a key regulator of an interaction between pCAR1 and its host Pseudomonas putida KT2440. KT2440 has two transcribed genes that encode the MvaT-like proteins TurA and TurB. Our previous transcriptome analyses suggested that the functions of Pmr, TurA and TurB are non-equivalent, although the detailed underlying mechanisms remain unclear. In this study, we focused on the protein–protein interactions of Pmr, and assessed the homo-oligomerization capacity of various substituted and truncated Pmr derivatives by protein–protein cross-linking analysis. Six of the seven residues identified as important for homo-oligomerization in Pmr were located near the N-terminus, and the putative flexible linker or the region near that was not involved in homo-oligomerization, suggesting that Pmr homo-oligomerization is different from that of enterobacterial H-NS and that the functional mechanism differs between H-NS-like and MvaT-like proteins. In addition, we assessed homo- and hetero-oligomerization of Pmr by surface plasmon resonance analysis and found that the coupling ratio of TurB-Pmr oligomers is smaller than that of Pmr-Pmr or TurA-Pmr oligomers. These results raised the possibility that composition of the hetero-oligomers of Pmr, TurA, and TurB could explain why the different gene sets were affected by either pmr, turA, or turB disruption in our previous studies.
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Affiliation(s)
- Chiho Suzuki
- Biotechnology Research Center, The University of Tokyo, Tokyo, Japan
| | - Kohei Kawazuma
- Biotechnology Research Center, The University of Tokyo, Tokyo, Japan
| | - Shoichiro Horita
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Tohru Terada
- Agricultural Bioinformatics Research Unit, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Masaru Tanokura
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Kazunori Okada
- Biotechnology Research Center, The University of Tokyo, Tokyo, Japan
| | - Hisakazu Yamane
- Biotechnology Research Center, The University of Tokyo, Tokyo, Japan
| | - Hideaki Nojiri
- Biotechnology Research Center, The University of Tokyo, Tokyo, Japan
- Agricultural Bioinformatics Research Unit, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
- * E-mail:
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35
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The functional structure of central carbon metabolism in Pseudomonas putida KT2440. Appl Environ Microbiol 2014; 80:5292-303. [PMID: 24951791 DOI: 10.1128/aem.01643-14] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
What defines central carbon metabolism? The classic textbook scheme of central metabolism includes the Embden-Meyerhof-Parnas (EMP) pathway of glycolysis, the pentose phosphate pathway, and the citric acid cycle. The prevalence of this definition of central metabolism is, however, equivocal without experimental validation. We address this issue using a general experimental approach that combines the monitoring of transcriptional and metabolic flux changes between steady states on alternative carbon sources. This approach is investigated by using the model bacterium Pseudomonas putida with glucose, fructose, and benzoate as carbon sources. The catabolic reactions involved in the initial uptake and metabolism of these substrates are expected to show a correlated change in gene expressions and metabolic fluxes. However, there was no correlation for the reactions linking the 12 biomass precursor molecules, indicating a regulation mechanism other than mRNA synthesis for central metabolism. This result substantiates evidence for a (re)definition of central carbon metabolism including all reactions that are bound to tight regulation and transcriptional invariance. Contrary to expectations, the canonical Entner-Doudoroff and EMP pathways sensu stricto are not a part of central carbon metabolism in P. putida, as they are not regulated differently from the aromatic degradation pathway. The regulatory analyses presented here provide leads on a qualitative basis to address the use of alternative carbon sources by deregulation and overexpression at the transcriptional level, while rate improvements in central carbon metabolism require careful adjustment of metabolite concentrations, as regulation resides to a large extent in posttranslational and/or metabolic regulation.
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Moreno R, Hernández-Arranz S, La Rosa R, Yuste L, Madhushani A, Shingler V, Rojo F. The Crc and Hfq proteins of Pseudomonas putida cooperate in catabolite repression and formation of ribonucleic acid complexes with specific target motifs. Environ Microbiol 2014; 17:105-18. [PMID: 24803210 DOI: 10.1111/1462-2920.12499] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Accepted: 04/28/2014] [Indexed: 12/22/2022]
Abstract
The Crc protein is a global regulator that has a key role in catabolite repression and optimization of metabolism in Pseudomonads. Crc inhibits gene expression post-transcriptionally, preventing translation of mRNAs bearing an AAnAAnAA motif [the catabolite activity (CA) motif] close to the translation start site. Although Crc was initially believed to bind RNA by itself, this idea was recently challenged by results suggesting that a protein co-purifying with Crc, presumably the Hfq protein, could account for the detected RNA-binding activity. Hfq is an abundant protein that has a central role in post-transcriptional gene regulation. Herein, we show that the Pseudomonas putida Hfq protein can recognize the CA motifs of RNAs through its distal face and that Crc facilitates formation of a more stable complex at these targets. Crc was unable to bind RNA in the absence of Hfq. However, pull-down assays showed that Crc and Hfq can form a co-complex with RNA containing a CA motif in vitro. Inactivation of the hfq or the crc gene impaired catabolite repression to a similar extent. We propose that Crc and Hfq cooperate in catabolite repression, probably through forming a stable co-complex with RNAs containing CA motifs to result in inhibition of translation initiation.
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Affiliation(s)
- Renata Moreno
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Darwin 3, Cantoblanco, 28049, Madrid, Spain
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Pflüger-Grau K, de Lorenzo V. From the phosphoenolpyruvate phosphotransferase system to selfish metabolism: a story retraced in Pseudomonas putida. FEMS Microbiol Lett 2014; 356:144-53. [PMID: 24801646 DOI: 10.1111/1574-6968.12459] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Revised: 04/28/2014] [Accepted: 04/30/2014] [Indexed: 12/17/2022] Open
Abstract
Although DNA is the ultimate repository of biological information, deployment of its instructions is constrained by the metabolic and physiological status of the cell. To this end, bacteria have evolved intricate devices that connect exogenous signals (e.g. nutrients, physicochemical conditions) with endogenous conditions (metabolic fluxes, biochemical networks) that coordinately influence expression or performance of a large number of cellular functions. The phosphoenolpyruvate:carbohydrate-phosphotransferase system (PTS) is a bacterial multi-protein phosphorylation chain which computes extracellular (e.g. sugars) and intracellular (e.g. phosphoenolpyruvate, nitrogen) signals and translates them into post-translational regulation of target activities through protein-protein interactions. The PTS of Pseudomonas putida KT2440 encompasses one complete sugar (fructose)-related system and the three enzymes that form the so-called nitrogen-related PTS (PTS(N) (tr) ), which lacks connection to transport of substrates. These two PTS branches cross-talk to each other, as the product of the fruB gene (a polyprotein EI-HPr-EIIA) can phosphorylate PtsN (EIIA(N) (tr) ) in vivo. This gives rise to a complex actuator device where diverse physiological inputs are ultimately translated into phosphorylation or not of PtsN (EIIA(N) (tr) ) which, in turn, checks the activity of key metabolic and regulatory proteins. Such a control of bacterial physiology highlights the prominence of biochemical homeostasis over genetic ruling -and not vice versa.
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Páez-Espino AD, Durante-Rodríguez G, de Lorenzo V. Functional coexistence of twin arsenic resistance systems in Pseudomonas putida KT2440. Environ Microbiol 2014; 17:229-38. [PMID: 24673935 DOI: 10.1111/1462-2920.12464] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Revised: 03/16/2014] [Accepted: 03/21/2014] [Indexed: 01/12/2023]
Abstract
The genome of the soil bacterium Pseudomonas putida KT2440 bears two virtually identical arsRBCH operons putatively encoding resistance to inorganic arsenic species. Single and double chromosomal deletions in each of these ars clusters of this bacterium were tested for arsenic sensitivity and found that the contribution of each operon to the resistance to the metalloid was not additive, as either cluster sufficed to endow cells with high-level resistance. However, otherwise identical traits linked to each of the ars sites diverged when temperature was decreased. Growth of the various mutants at 15°C (instead of the standard 30°C for P. putida) uncovered that ars2 affords a much higher resistance to As (III) than the ars1 counterpart. Reverse transcription polymerase chain reaction of arsB1 and arsB2 genes as well as lacZ fusions to the Pars1 and Pars2 promoters traced the difference to variations in transcription of the corresponding gene sets at each temperature. Functional redundancy may thus be selected as a stable condition - rather than just as transient state - if it affords one key activity to be expressed under a wider range of physicochemical settings. This seems to provide a straightforward solution to regulatory problems in environmental bacteria that thrive under changing scenarios.
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Affiliation(s)
- A David Páez-Espino
- Centro Nacional de Biotecnología-CSIC, Campus de Cantoblanco, Madrid, 28049, Spain
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Molina-Santiago C, Daddaoua A, Fillet S, Duque E, Ramos JL. Interspecies signalling: Pseudomonas putida efflux pump TtgGHI is activated by indole to increase antibiotic resistance. Environ Microbiol 2014; 16:1267-81. [PMID: 24373097 DOI: 10.1111/1462-2920.12368] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2013] [Accepted: 12/14/2013] [Indexed: 12/13/2022]
Abstract
In Gram-negative bacteria, multidrug efflux pumps are responsible for the extrusion of chemicals that are deleterious for growth. Some of these efflux pumps are induced by endogenously produced effectors, while abiotic or biotic signals induce the expression of other efflux pumps. In Pseudomonas putida, the TtgABC efflux pump is the main antibiotic extrusion system that respond to exogenous antibiotics through the modulation of the expression of this operon mediated by TtgR. The plasmid-encoded TtgGHI efflux pump in P. putida plays a minor role in antibiotic resistance in the parental strain; however, its role is critical in isogenic backgrounds deficient in TtgABC. Expression of ttgGHI is repressed by the TtgV regulator that recognizes indole as an effector, although P. putida does not produce indole itself. Because indole is not produced by Pseudomonas, the indole-dependent antibiotic resistance seems to be part of an antibiotic resistance programme at the community level. Pseudomonas putida recognizes indole added to the medium or produced by Escherichia coli in mixed microbial communities. Transcriptomic analyses revealed that the indole-specific response involves activation of 43 genes and repression of 23 genes. Indole enhances not only the expression of the TtgGHI pump but also a set of genes involved in iron homeostasis, as well as genes for amino acid catabolism. In a ttgABC-deficient P. putida, background ampicillin and other bactericidal compounds lead to cell death. Co-culture of E. coli and P. putida ΔttgABC allowed growth of the P. putida mutant in the presence of ampicillin because of induction of the indole-dependent efflux pump.
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Affiliation(s)
- Carlos Molina-Santiago
- Consejo Superior de Investigaciones Científicas, Estación Experimental del Zaidín, 18008, Granada, Spain
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40
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Tomás-Gallardo L, Gómez-Álvarez H, Santero E, Floriano B. Combination of degradation pathways for naphthalene utilization in Rhodococcus sp. strain TFB. Microb Biotechnol 2013; 7:100-13. [PMID: 24325207 PMCID: PMC3937715 DOI: 10.1111/1751-7915.12096] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2013] [Revised: 10/03/2013] [Accepted: 10/07/2013] [Indexed: 11/27/2022] Open
Abstract
Rhodococcus sp. strain TFB is a metabolic versatile bacterium able to grow on naphthalene as the only carbon and energy source. Applying proteomic, genetic and biochemical approaches, we propose in this paper that, at least, three coordinated but independently regulated set of genes are combined to degrade naphthalene in TFB. First, proteins involved in tetralin degradation are also induced by naphthalene and may carry out its conversion to salicylaldehyde. This is the only part of the naphthalene degradation pathway showing glucose catabolite repression. Second, a salicylaldehyde dehydrogenase activity that converts salicylaldehyde to salicylate is detected in naphthalene-grown cells but not in tetralin-or salicylate-grown cells. Finally, we describe the chromosomally located nag genes, encoding the gentisate pathway for salicylate conversion into fumarate and pyruvate, which are only induced by salicylate and not by naphthalene. This work shows how biodegradation pathways in Rhodococcus sp. strain TFB could be assembled using elements from different pathways mainly because of the laxity of the regulatory systems and the broad specificity of the catabolic enzymes.
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Affiliation(s)
- Laura Tomás-Gallardo
- Centro Andaluz de Biología del Desarrollo, CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
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Sevilla E, Alvarez-Ortega C, Krell T, Rojo F. The Pseudomonas putida HskA hybrid sensor kinase responds to redox signals and contributes to the adaptation of the electron transport chain composition in response to oxygen availability. ENVIRONMENTAL MICROBIOLOGY REPORTS 2013; 5:825-834. [PMID: 24249291 DOI: 10.1111/1758-2229.12083] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Accepted: 06/22/2013] [Indexed: 06/02/2023]
Abstract
Pseudomonas putida has a branched aerobic electron transport that includes five terminal oxidases, each of which has different properties. The relative expression of each oxidase is carefully regulated to assemble the most suitable electron transport chain for the prevailing conditions. The HskA hybrid sensor kinase participates in this control, but the signals to which HskA responds were unknown. Here, the influence of HskA on the mRNA abundance of genes coding for all terminal oxidases and for the bc1 complex was analysed in cells growing under controlled aerobic, semiaerobic or microaerobic conditions. The results indicate that the influence of HskA on the expression of each terminal oxidase and the bc1 complex varies depending on oxygen availability. This effect was more pronounced under aerobic or semiaerobic conditions, but decreased under microaerobic conditions. The expression of hskA was regulated by oxygen availability. We show that HskA autophosphorylation is inhibited by ubiquinone but not by ubiquinol, its reduced derivative. This suggests that HskA could sense the oxidation state of the respiratory ubiquinones, which may be a key factor in HskA activity. Inactivation of hskA reduced growth rate and oxygen consumption, stressing the importance of HskA for the assembly of an efficient electron transport chain.
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Affiliation(s)
- Emma Sevilla
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Campus UAM, Cantoblanco, 28049, Madrid, Spain
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La Rosa R, de la Peña F, Prieto MA, Rojo F. The Crc protein inhibits the production of polyhydroxyalkanoates inPseudomonas putidaunder balanced carbon/nitrogen growth conditions. Environ Microbiol 2013; 16:278-90. [DOI: 10.1111/1462-2920.12303] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Accepted: 10/02/2013] [Indexed: 11/27/2022]
Affiliation(s)
- Ruggero La Rosa
- Departamento de Biotecnología Microbiana; Centro Nacional de Biotecnología, CSIC; Darwin 3 Cantoblanco 28049 Madrid Spain
| | - Fernando de la Peña
- Departamento de Biología Ambiental; Centro de Investigaciones Biológicas, CSIC; Ramiro de Maeztu 9 28040 Madrid Spain
| | - María Axiliadora Prieto
- Departamento de Biología Ambiental; Centro de Investigaciones Biológicas, CSIC; Ramiro de Maeztu 9 28040 Madrid Spain
| | - Fernando Rojo
- Departamento de Biotecnología Microbiana; Centro Nacional de Biotecnología, CSIC; Darwin 3 Cantoblanco 28049 Madrid Spain
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García-Mauriño SM, Pérez-Martínez I, Amador CI, Canosa I, Santero E. Transcriptional activation of the CrcZ and CrcY regulatory RNAs by the CbrB response regulator in Pseudomonas putida. Mol Microbiol 2013; 89:189-205. [PMID: 23692431 DOI: 10.1111/mmi.12270] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/17/2013] [Indexed: 11/30/2022]
Abstract
The CbrAB two-component system has been described as a high-ranked element in the regulatory hierarchy of Pseudomonas putida that controls a variety of metabolic and behavioural traits required for adaptation to changing environmental conditions. We show that the response regulatory protein CbrB, an activator of σ(N) -dependent promoters, directly controls the expression of the small RNAs CrcZ and CrcY in P. putida. These two RNAs sequester the protein Crc, which is a translational repressor of multiple pathways linked to carbon catabolite repression. We characterized the in vivo and in vitro activation by CbrB at both crcZ and crcY promoters, and identified new DNA sequences where the protein binds. IHF, a co-activator at many σ(N) -dependent promoters, also binds to the promoter regions and contributes to the activation of the sRNAs. CbrB phosphorylation is necessary at physiological activation conditions, but a higher dose of the protein allows in vitro transcriptional activation in its non-phosphorylated form. We also show there is some production of CrcY coming from an upstream promoter independent of CbrB. Thus, CbrAB constitute a global signal transduction pathway integrated in a higher regulatory network that also controls catabolite repression through the expression of the two regulatory RNAs CrcZ and CrcY.
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Affiliation(s)
- Sofía Muñoz García-Mauriño
- Centro Andaluz de Biología del Desarrollo, CSIC, Universidad Pablo de Olavide, Carretera de Utrera, Km. 1, 41013, Seville, Spain
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Sevilla E, Silva-Jiménez H, Duque E, Krell T, Rojo F. The Pseudomonas putida HskA hybrid sensor kinase controls the composition of the electron transport chain. ENVIRONMENTAL MICROBIOLOGY REPORTS 2013; 5:291-300. [PMID: 23584971 DOI: 10.1111/1758-2229.12017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Accepted: 11/13/2012] [Indexed: 06/02/2023]
Abstract
Sensor kinases play a key role in sensing and responding to environmental and physiological signals in bacteria. In this study we characterized a previously unknown orphan hybrid sensor kinase from Pseudomonas putida, which is conserved in several Pseudomonads. Inactivation of the gene coding for this sensor kinase, which we have named HskA, modified the expression of at least 85 genes in cells growing in a complete medium. HskA showed a strong influence on the composition of the electron transport chain. In cells growing exponentially in a complete medium, the absence of HskA led to a significant reduction in the expression of the genes coding for the bc1 complex and for the CIO and Cbb3-1 terminal oxidases. In stationary phase cells, however, lack of HskA caused a higher expression of the Cyo terminal oxidase and a lower expression of the Aa3 terminal oxidase. The HskA polypeptide shows two PAS (signal-sensing) domains, a transmitter domain containing the invariant phosphorylatable histidine and an ATP binding site, and a receiver domain containing the conserved aspartate capable of transphosphorylation, but lacks an Hpt module. It is therefore a hybrid sensor kinase. Phosphorylation assays showed that purified HskA undergoes autophosphorylation in the presence of ATP.
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Affiliation(s)
- Emma Sevilla
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Campus UAM, Cantoblanco, 28049 Madrid, Spain
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Follonier S, Escapa IF, Fonseca PM, Henes B, Panke S, Zinn M, Prieto MA. New insights on the reorganization of gene transcription in Pseudomonas putida KT2440 at elevated pressure. Microb Cell Fact 2013; 12:30. [PMID: 23537069 PMCID: PMC3621253 DOI: 10.1186/1475-2859-12-30] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Accepted: 02/21/2013] [Indexed: 11/17/2022] Open
Abstract
Background Elevated pressure, elevated oxygen tension (DOT) and elevated carbon dioxide tension (DCT) are readily encountered at the bottom of large industrial bioreactors and during bioprocesses where pressure is applied for enhancing the oxygen transfer. Yet information about their effect on bacteria and on the gene expression thereof is scarce. To shed light on the cellular functions affected by these specific environmental conditions, the transcriptome of Pseudomonas putida KT2440, a bacterium of great relevance for the production of medium-chain-length polyhydroxyalkanoates, was thoroughly investigated using DNA microarrays. Results Very well defined chemostat cultivations were carried out with P. putida to produce high quality RNA samples and ensure that differential gene expression was caused exclusively by changes of pressure, DOT and/or DCT. Cellular stress was detected at 7 bar and elevated DCT in the form of heat shock and oxidative stress-like responses, and indicators of cell envelope perturbations were identified as well. Globally, gene transcription was not considerably altered when DOT was increased from 40 ± 5 to 235 ± 20% at 7 bar and elevated DCT. Nevertheless, differential transcription was observed for a few genes linked to iron-sulfur cluster assembly, terminal oxidases, glutamate metabolism and arginine deiminase pathway, which shows their particular sensitivity to variations of DOT. Conclusions This study provides a comprehensive overview on the changes occurring in the transcriptome of P. putida upon mild variations of pressure, DOT and DCT. Interestingly, whereas the changes of gene transcription were widespread, the cell physiology was hardly affected, which illustrates how efficient reorganization of the gene transcription is for dealing with environmental changes that may otherwise be harmful. Several particularly sensitive cellular functions were identified, which will certainly contribute to the understanding of the mechanisms involved in stress sensing/response and to finding ways of enhancing the stress tolerance of microorganisms.
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Affiliation(s)
- Stéphanie Follonier
- Swiss Federal Laboratories for Materials Science and Technology, Gallen, Switzerland
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46
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An in vitro study of Lactobacillus plantarum strains for the presence of plantaricin genes and their potential control of the table olive microbiota. Antonie Van Leeuwenhoek 2012; 103:821-32. [DOI: 10.1007/s10482-012-9864-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Accepted: 12/01/2012] [Indexed: 10/27/2022]
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Hernández-Arranz S, Moreno R, Rojo F. The translational repressor Crc controls the Pseudomonas putida benzoate and alkane catabolic pathways using a multi-tier regulation strategy. Environ Microbiol 2012; 15:227-41. [PMID: 22925411 DOI: 10.1111/j.1462-2920.2012.02863.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Revised: 07/27/2012] [Accepted: 07/29/2012] [Indexed: 11/28/2022]
Abstract
Metabolically versatile bacteria usually perceive aromatic compounds and hydrocarbons as non-preferred carbon sources, and their assimilation is inhibited if more preferable substrates are available. This is achieved via catabolite repression. In Pseudomonas putida, the expression of the genes allowing the assimilation of benzoate and n-alkanes is strongly inhibited by catabolite repression, a process controlled by the translational repressor Crc. Crc binds to and inhibits the translation of benR and alkS mRNAs, which encode the transcriptional activators that induce the expression of the benzoate and alkane degradation genes respectively. However, sequences similar to those recognized by Crc in benR and alkS mRNAs exist as well in the translation initiation regions of the mRNA of several structural genes of the benzoate and alkane pathways, which suggests that Crc may also regulate their translation. The present results show that some of these sites are functional, and that Crc inhibits the induction of both pathways by limiting not only the translation of their transcriptional activators, but also that of genes coding for the first enzyme in each pathway. Crc may also inhibit the translation of a gene involved in benzoate uptake. This multi-tier approach probably ensures the rapid regulation of pathway genes, minimizing the assimilation of non-preferred substrates when better options are available. A survey of possible Crc sites in the mRNAs of genes associated with other catabolic pathways suggested that targeting substrate uptake, pathway induction and/or pathway enzymes may be a common strategy to control the assimilation of non-preferred compounds.
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Affiliation(s)
- Sofía Hernández-Arranz
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Campus UAM, Cantoblanco, 28049 Madrid, Spain
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Fernández M, Niqui-Arroyo JL, Conde S, Ramos JL, Duque E. Enhanced tolerance to naphthalene and enhanced rhizoremediation performance for Pseudomonas putida KT2440 via the NAH7 catabolic plasmid. Appl Environ Microbiol 2012; 78:5104-10. [PMID: 22582075 PMCID: PMC3416403 DOI: 10.1128/aem.00619-12] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Accepted: 05/04/2012] [Indexed: 01/16/2023] Open
Abstract
In this work, we explore the potential use of the Pseudomonas putida KT2440 strain for bioremediation of naphthalene-polluted soils. Pseudomonas putida strain KT2440 thrives in naphthalene-saturated medium, establishing a complex response that activates genes coding for extrusion pumps and cellular damage repair enzymes, as well as genes involved in the oxidative stress response. The transfer of the NAH7 plasmid enables naphthalene degradation by P. putida KT2440 while alleviating the cellular stress brought about by this toxic compound, without affecting key functions necessary for survival and colonization of the rhizosphere. Pseudomonas putida KT2440(NAH7) efficiently expresses the Nah catabolic pathway in vitro and in situ, leading to the complete mineralization of [(14)C]naphthalene, measured as the evolution of (14)CO(2), while the rate of mineralization was at least 2-fold higher in the rhizosphere than in bulk soil.
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Affiliation(s)
| | | | - Susana Conde
- Bio-Iliberis Research and Development, Granada, Spain
| | - Juan Luis Ramos
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Estrella Duque
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
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Metaproteogenomic insights beyond bacterial response to naphthalene exposure and bio-stimulation. ISME JOURNAL 2012; 7:122-36. [PMID: 22832345 PMCID: PMC3526184 DOI: 10.1038/ismej.2012.82] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Microbial metabolism in aromatic-contaminated environments has important ecological implications, and obtaining a complete understanding of this process remains a relevant goal. To understand the roles of biodiversity and aromatic-mediated genetic and metabolic rearrangements, we conducted ‘OMIC' investigations in an anthropogenically influenced and polyaromatic hydrocarbon (PAH)-contaminated soil with (Nbs) or without (N) bio-stimulation with calcium ammonia nitrate, NH4NO3 and KH2PO4 and the commercial surfactant Iveysol, plus two naphthalene-enriched communities derived from both soils (CN2 and CN1, respectively). Using a metagenomic approach, a total of 52, 53, 14 and 12 distinct species (according to operational phylogenetic units (OPU) in our work equivalent to taxonomic species) were identified in the N, Nbs, CN1 and CN2 communities, respectively. Approximately 10 out of 95 distinct species and 238 out of 3293 clusters of orthologous groups (COGs) protein families identified were clearly stimulated under the assayed conditions, whereas only two species and 1465 COGs conformed to the common set in all of the mesocosms. Results indicated distinct biodegradation capabilities for the utilisation of potential growth-supporting aromatics, which results in bio-stimulated communities being extremely fit to naphthalene utilisation and non-stimulated communities exhibiting a greater metabolic window than previously predicted. On the basis of comparing protein expression profiles and metagenome data sets, inter-alia interactions among members were hypothesised. The utilisation of curated databases is discussed and used for first time to reconstruct ‘presumptive' degradation networks for complex microbial communities.
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Chavarría M, Fuhrer T, Sauer U, Pflüger-Grau K, de Lorenzo V. Cra regulates the cross-talk between the two branches of the phosphoenolpyruvate : phosphotransferase system of Pseudomonas putida. Environ Microbiol 2012; 15:121-32. [PMID: 22708906 DOI: 10.1111/j.1462-2920.2012.02808.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The gene that encodes the catabolite repressor/activator, Cra (FruR), of Pseudomonas putida is divergent from the fruBKA operon for the uptake of fructose via the phosphoenolpyruvate : carbohydrate phosphotransferase system (PTS(Fru)). The expression of the fru cluster has been studied in cells growing on substrates that change the intracellular concentrations of fructose-1-P (F1P), the principal metabolic intermediate that counteracts the DNA-binding ability of Cra on an upstream operator. While the levels of the regulator were not affected by any of the growth conditions tested, the transcription of fruB was stimulated by fructose but not by the gluconeogenic substrate, succinate. The analysis of the P(fruB) promoter activity in a strain lacking the Cra protein and the determination of key metabolites revealed that this regulator represses the expression of PTS(Fru) in a fashion that is dependent on the endogenous concentrations of F1P. Because FruB (i.e. the EI-HPr-EIIA(Fru) polyprotein) can deliver a high-energy phosphate to the EIIA(Ntr) (PtsN) enzyme of the PTS(Ntr) branch, the cross-talk between the two phosphotransferase systems was examined under metabolic regimes that allowed for the high or low transcription of the fruBKA operon. While fructose caused cross-talk, succinate prevented it almost completely. Furthermore, PtsN phosphorylation by FruB occurred in a Δcra mutant regardless of growth conditions. These results traced the occurrence of the cross-talk to intracellular pools of Cra effectors, in particular F1P. The Cra/F1P duo seems to not only control the expression of the PTS(Fru) but also checks the activity of the PTS(Ntr) in vivo.
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Affiliation(s)
- Max Chavarría
- Systems Biology Program, Centro Nacional de Biotecnología, 28049 Cantoblanco-Madrid, Spain
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