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Yu XQ, Yan X, Zhang MY, Zhang LQ, He YX. Flavonoids repress the production of antifungal 2,4-DAPG but potentially facilitate root colonization of the rhizobacterium Pseudomonas fluorescens. Environ Microbiol 2020; 22:5073-5089. [PMID: 32363709 DOI: 10.1111/1462-2920.15052] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Accepted: 04/28/2020] [Indexed: 11/25/2022]
Abstract
In the well-known legume-rhizobia symbiosis, flavonoids released by legume roots induce expression of the Nod factors and trigger early plant responses involved in root nodulation. However, it remains largely unknown how the plant-derived flavonoids influence the physiology of non-symbiotic beneficial rhizobacteria. In this work, we demonstrated that the flavonoids apigenin and/or phloretin enhanced the swarming motility and production of cellulose and curli in Pseudomonas fluorescens 2P24, both traits of which are essential for root colonization. Using a label-free quantitative proteomics approach, we showed that apigenin and phloretin significantly reduced the biosynthesis of the antifungal metabolite 2,4-DAPG and further identified a novel flavonoid-sensing TetR regulator PhlH, which was shown to modulate 2,4-DAPG production by regulating the expression of 2,4-DAPG hydrolase PhlG. Although having similar structures, apigenin and phloretin could also influence different physiological characteristics of P. fluorescens 2P24, with apigenin decreasing the biofilm formation and phloretin inducing expression of proteins involved in the denitrification and arginine fermentation processes. Taken together, our results suggest that plant-derived flavonoids could be sensed by the TetR regulator PhlH in P. fluorescens 2P24 and acts as important signalling molecules that strengthen mutually beneficial interactions between plants and non-symbiotic beneficial rhizobacteria.
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Affiliation(s)
- Xiao-Quan Yu
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Xu Yan
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Meng-Yuan Zhang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Li-Qun Zhang
- Department of Plant Pathology, China Agricultural University, Beijing, China
| | - Yong-Xing He
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
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Oxidative stress under low oxygen conditions triggers hyperflagellation and motility in the Antarctic bacterium Pseudomonas extremaustralis. Extremophiles 2019; 23:587-597. [PMID: 31250111 DOI: 10.1007/s00792-019-01110-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 06/17/2019] [Indexed: 12/14/2022]
Abstract
Reactive oxygen species and nitrogen species (ROS and RNS), produced in a wide range of physiological process even under low oxygen availability, are among the main stressors found in the environment. Strategies developed to combat them constitute key features in bacterial adaptability and survival. Pseudomonas extremaustralis is a metabolic versatile and stress resistant Antarctic bacterium, able to grow under different oxygen conditions. The present work explores the effect of oxidative stress under low oxygen conditions in P. extremaustralis, by combining RNA deep sequencing analysis and physiological studies. Cells grown under microaerobiosis exhibited more oxidative damage in macromolecules and lower survival rates than under aerobiosis. RNA-seq analysis showed an up-regulation of genes related with oxidative stress response, flagella, chemotaxis and biofilm formation while chaperones and cytochromes were down-regulated. Microaerobic cultures exposed to H2O2 also displayed a hyper-flagellated phenotype coupled with a high motility behavior. Moreover, cells that were subjected to oxidative stress presented increased biofilm formation. Altogether, our results suggest that a higher motile behavior and augmented capacity to form biofilm structures could work in addition to well-known antioxidant enzymes and non-enzymatic ROS scavenging mechanisms to cope with oxidative stress at low oxygen tensions.
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Tribelli PM, Lujan AM, Pardo A, Ibarra JG, Fernández Do Porto D, Smania A, López NI. Core regulon of the global anaerobic regulator Anr targets central metabolism functions in Pseudomonas species. Sci Rep 2019; 9:9065. [PMID: 31227753 PMCID: PMC6588701 DOI: 10.1038/s41598-019-45541-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 06/07/2019] [Indexed: 12/19/2022] Open
Abstract
A comparative genome analysis of the global anaerobic regulator Anr regulon in five species of Pseudomonas with different life style was performed. Expression of this regulator was detected in all analyzed Pseudomonas. The predicted Anr regulon (pan-regulon) consisted of 253 genes. However, only 11 Anr-boxes located upstream of qor/hemF, hemN, cioA/PA3931, azu, rpsL, gltP, orthologous to PA2867, cspD, tyrZ, slyD and oprG, were common to all species. Whole genome in silico prediction of metabolic pathways identified genes belonging to heme biosynthesis, cytochromes and Entner-Doudoroff pathway as members of Anr regulon in all strains. Extending genome analysis to 28 Pseudomonas spp. spanning all phylogenetic groups showed Anr-boxes conservation in genes related to these functions. When present, genes related to anaerobic metabolism were predicted to hold Anr-boxes. Focused on the genomes of eight P. aeruginosa isolates of diverse origins, we observed a conserved regulon, sharing nearly 80% of the genes, indicating its key role in this opportunistic pathogen. The results suggest that the core Anr regulon comprises genes involved in central metabolism and aerobic electron transport chain, whereas those genes related to anaerobic metabolism and other functions constitute the accessory Anr-regulon, thereby differentially contributing to the ecological fitness of each Pseudomonas species.
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Affiliation(s)
- Paula M Tribelli
- IQUIBICEN, CONICET, Universidad de Buenos Aires, Buenos Aires, Argentina.,Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Adela M Lujan
- Universidad Nacional de Córdoba, Facultad de Ciencias Químicas, Departamento de Química Biológica Ranwel Caputto, Córdoba, Argentina.,CONICET, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), Córdoba, Argentina
| | - Agustín Pardo
- IQUIBICEN, CONICET, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - José G Ibarra
- IQUIBICEN, CONICET, Universidad de Buenos Aires, Buenos Aires, Argentina
| | | | - Andrea Smania
- Universidad Nacional de Córdoba, Facultad de Ciencias Químicas, Departamento de Química Biológica Ranwel Caputto, Córdoba, Argentina.,CONICET, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), Córdoba, Argentina
| | - Nancy I López
- IQUIBICEN, CONICET, Universidad de Buenos Aires, Buenos Aires, Argentina. .,Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.
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Benforte FC, Colonnella MA, Ricardi MM, Solar Venero EC, Lizarraga L, López NI, Tribelli PM. Novel role of the LPS core glycosyltransferase WapH for cold adaptation in the Antarctic bacterium Pseudomonas extremaustralis. PLoS One 2018; 13:e0192559. [PMID: 29415056 PMCID: PMC5802925 DOI: 10.1371/journal.pone.0192559] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2017] [Accepted: 01/25/2018] [Indexed: 11/19/2022] Open
Abstract
Psychrotroph microorganisms have developed cellular mechanisms to cope with cold stress. Cell envelopes are key components for bacterial survival. Outer membrane is a constituent of Gram negative bacterial envelopes, consisting of several components, such as lipopolysaccharides (LPS). In this work we investigated the relevance of envelope characteristics for cold adaptation in the Antarctic bacterium Pseudomonas extremaustralis by analyzing a mini Tn5 wapH mutant strain, encoding a core LPS glycosyltransferase. Our results showed that wapH strain is impaired to grow under low temperature but not for cold survival. The mutation in wapH, provoked a strong aggregative phenotype and modifications of envelope nanomechanical properties such as lower flexibility and higher turgor pressure, cell permeability and surface area to volume ratio (S/V). Changes in these characteristics were also observed in the wild type strain grown at different temperatures, showing higher cell flexibility but lower turgor pressure under cold conditions. Cold shock experiments indicated that an acclimation period in the wild type is necessary for cell flexibility and S/V ratio adjustments. Alteration in cell-cell interaction capabilities was observed in wapH strain. Mixed cells of wild type and wapH strains, as well as those of the wild type strain grown at different temperatures, showed a mosaic pattern of aggregation. These results indicate that wapH mutation provoked marked envelope alterations showing that LPS core conservation appears as a novel essential feature for active growth under cold conditions.
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Affiliation(s)
- Florencia C. Benforte
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Maria A. Colonnella
- Centro de Investigaciones en Bionanociencias, CONICET, Buenos Aires, Argentina
| | - Martiniano M. Ricardi
- Instituto de Fisiología, Biología Molecular y Neurociencias, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | | | - Leonardo Lizarraga
- Centro de Investigaciones en Bionanociencias, CONICET, Buenos Aires, Argentina
| | - Nancy I. López
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- IQUIBICEN, CONICET, Buenos Aires, Argentina
- * E-mail: (NIL); (PMT)
| | - Paula M. Tribelli
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- IQUIBICEN, CONICET, Buenos Aires, Argentina
- * E-mail: (NIL); (PMT)
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Tribelli PM, Rossi L, Ricardi MM, Gomez-Lozano M, Molin S, Raiger Iustman LJ, Lopez NI. Microaerophilic alkane degradation in Pseudomonas extremaustralis: a transcriptomic and physiological approach. ACTA ACUST UNITED AC 2018; 45:15-23. [DOI: 10.1007/s10295-017-1987-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 11/01/2017] [Indexed: 01/25/2023]
Abstract
Abstract
Diesel fuel is one of the most important sources of hydrocarbon contamination worldwide. Its composition consists of a complex mixture of n-alkanes, branched alkanes and aromatic compounds. Hydrocarbon degradation in Pseudomonas species has been mostly studied under aerobic conditions; however, a dynamic spectrum of oxygen availability can be found in the environment. Pseudomonas extremaustralis, an Antarctic bacterium isolated from a pristine environment, is able to degrade diesel fuel and presents a wide microaerophilic metabolism. In this work RNA-deep sequence experiments were analyzed comparing the expression profile in aerobic and microaerophilic cultures. Interestingly, genes involved in alkane degradation, including alkB, were over-expressed in micro-aerobiosis in absence of hydrocarbon compounds. In minimal media supplemented with diesel fuel, n-alkanes degradation (C13–C19) after 7 days was observed under low oxygen conditions but not in aerobiosis. In-silico analysis of the alkB promoter zone showed a putative binding sequence for the anaerobic global regulator, Anr. Our results indicate that some diesel fuel components can be utilized as sole carbon source under microaerophilic conditions for cell maintenance or slow growth in a Pseudomonas species and this metabolism could represent an adaptive advantage in polluted environments.
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Affiliation(s)
- Paula M Tribelli
- 0000 0001 0056 1981 grid.7345.5 Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales Universidad de Buenos Aires Intendente Guiraldes, 2160 C1428EGA Buenos Aires Argentina
- 0000 0001 1945 2152 grid.423606.5 IQUIBICEN, CONICET Buenos Aires Argentina
| | - Leticia Rossi
- 0000 0001 1945 2152 grid.423606.5 IQUIBICEN, CONICET Buenos Aires Argentina
| | - Martiniano M Ricardi
- 0000 0001 0056 1981 grid.7345.5 Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-CONICET), Facultad de Ciencias Exactas y Naturales Universidad de Buenos Aires C1428EGA Buenos Aires Argentina
| | - Maria Gomez-Lozano
- 0000 0001 2181 8870 grid.5170.3 Novo Nordisk Foundation Center for Biosustainability Technical University of Denmark Hørsholm Denmark
| | - Søren Molin
- 0000 0001 2181 8870 grid.5170.3 Novo Nordisk Foundation Center for Biosustainability Technical University of Denmark Hørsholm Denmark
| | - Laura J Raiger Iustman
- 0000 0001 0056 1981 grid.7345.5 Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales Universidad de Buenos Aires Intendente Guiraldes, 2160 C1428EGA Buenos Aires Argentina
- 0000 0001 1945 2152 grid.423606.5 IQUIBICEN, CONICET Buenos Aires Argentina
| | - Nancy I Lopez
- 0000 0001 0056 1981 grid.7345.5 Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales Universidad de Buenos Aires Intendente Guiraldes, 2160 C1428EGA Buenos Aires Argentina
- 0000 0001 1945 2152 grid.423606.5 IQUIBICEN, CONICET Buenos Aires Argentina
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Tribelli PM, Solar Venero EC, Ricardi MM, Gómez-Lozano M, Raiger Iustman LJ, Molin S, López NI. Novel Essential Role of Ethanol Oxidation Genes at Low Temperature Revealed by Transcriptome Analysis in the Antarctic Bacterium Pseudomonas extremaustralis. PLoS One 2015; 10:e0145353. [PMID: 26671564 PMCID: PMC4686015 DOI: 10.1371/journal.pone.0145353] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 12/02/2015] [Indexed: 02/06/2023] Open
Abstract
Temperature is one of the most important factors for bacterial growth and development. Cold environments are widely distributed on earth, and psychrotolerant and psychrophilic microorganisms have developed different adaptation strategies to cope with the stress derived from low temperatures. Pseudomonas extremaustralis is an Antarctic bacterium able to grow under low temperatures and to produce high amounts of polyhydroxyalkanoates (PHAs). In this work, we analyzed the genome-wide transcriptome by RNA deep-sequencing technology of early exponential cultures of P. extremaustralis growing in LB (Luria Broth) supplemented with sodium octanoate to favor PHA accumulation at 8°C and 30°C. We found that genes involved in primary metabolism, including tricarboxylic acid cycle (TCA) related genes, as well as cytochromes and amino acid metabolism coding genes, were repressed at low temperature. Among up-regulated genes, those coding for transcriptional regulatory and signal transduction proteins were over-represented at cold conditions. Remarkably, we found that genes involved in ethanol oxidation, exaA, exaB and exaC, encoding a pyrroloquinoline quinone (PQQ)-dependent ethanol dehydrogenase, the cytochrome c550 and an aldehyde dehydrogenase respectively, were up-regulated. Along with RNA-seq experiments, analysis of mutant strains for pqqB (PQQ biosynthesis protein B) and exaA were carried out. We found that the exaA and pqqB genes are essential for growth under low temperature in LB supplemented with sodium octanoate. Additionally, p-rosaniline assay measurements showed the presence of alcohol dehydrogenase activity at both 8°C and 30°C, while the activity was abolished in a pqqB mutant strain. These results together with the detection of ethanol by gas chromatography in P. extremaustralis cultures grown at 8°C support the conclusion that this pathway is important under cold conditions. The obtained results have led to the identification of novel components involved in cold adaptation mechanisms in this bacterium, suggesting for the first time a role of the ethanol oxidation pathway for bacterial growth at low temperatures.
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Affiliation(s)
- Paula M. Tribelli
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Guiraldes 2160, C1428EGA Buenos Aires, Argentina
- IQUIBICEN, CONICET, Buenos Aires, Argentina
| | | | - Martiniano M. Ricardi
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-CONICET), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina
| | - Maria Gómez-Lozano
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
| | - Laura J. Raiger Iustman
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Guiraldes 2160, C1428EGA Buenos Aires, Argentina
- IQUIBICEN, CONICET, Buenos Aires, Argentina
| | - Søren Molin
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
| | - Nancy I. López
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Guiraldes 2160, C1428EGA Buenos Aires, Argentina
- IQUIBICEN, CONICET, Buenos Aires, Argentina
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Roles of RpoS in Yersinia pseudotuberculosis stress survival, motility, biofilm formation and type VI secretion system expression. J Microbiol 2015; 53:633-42. [DOI: 10.1007/s12275-015-0099-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Revised: 07/16/2015] [Accepted: 07/22/2015] [Indexed: 12/27/2022]
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Gómez-Lozano M, Marvig RL, Molina-Santiago C, Tribelli PM, Ramos JL, Molin S. Diversity of small RNAs expressed in Pseudomonas species. ENVIRONMENTAL MICROBIOLOGY REPORTS 2015; 7:227-236. [PMID: 25394275 DOI: 10.1111/1758-2229.12233] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Revised: 10/18/2014] [Accepted: 10/28/2014] [Indexed: 06/04/2023]
Abstract
RNA sequencing (RNA-seq) has revealed several hundreds of previously undetected small RNAs (sRNAs) in all bacterial species investigated, including strains of Pseudomonas aeruginosa, Pseudomonas putida and Pseudomonas syringae. Nonetheless, only little is known about the extent of conservation of expressed sRNAs across strains and species. In this study, we have used RNA-seq to identify sRNAs in P. putida DOT-T1E and Pseudomonas extremaustralis 14-3b. This is the first strain of P. extremaustralis and the second strain of P. putida to have their transcriptomes analysed for sRNAs, and we identify the presence of around 150 novel sRNAs in each strain. Furthermore, we provide a comparison based on sequence conservation of all the sRNAs detected by RNA-seq in the Pseudomonas species investigated so far. Our results show that the extent of sRNA conservation across different species is very limited. In addition, when comparing the sRNAs expressed in different strains of the same species, we observe that numerous sRNAs exhibit a strain-specific expression pattern. These results support the idea that the evolution of most bacterial sRNAs is rapid, which limits the extent of both interspecies and intraspecies conservation.
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Affiliation(s)
- María Gómez-Lozano
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, DK-2970, Denmark
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