47 results on '"Molina-Santiago C"'
Search Results
2. Bacillus subtilis biofilm matrix components target seed oil bodies to promote growth and anti-fungal resistance in melon
- Author
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Berlanga-Clavero, M.V., Molina-Santiago, C., Caraballo-Rodriguez, A. M., Petras, D., Diaz-Martinez, L., Perez-Garcia, A., de Vicente, A., Carrion, V. J., Dorrestein, P. C., Romero, D., Berlanga-Clavero, M.V., Molina-Santiago, C., Caraballo-Rodriguez, A. M., Petras, D., Diaz-Martinez, L., Perez-Garcia, A., de Vicente, A., Carrion, V. J., Dorrestein, P. C., and Romero, D.
- Abstract
Beneficial microorganisms are used to stimulate the germination of seeds; however, their growth-promoting mechanisms remain largely unexplored. Bacillus subtilis is commonly found in association with different plant organs, providing protection against pathogens or stimulating plant growth. We report that application of B. subtilis to melon seeds results in genetic and physiological responses in seeds that alter the metabolic and developmental status in 5-d and 1-month-old plants upon germination. We analysed mutants in different components of the extracellular matrix of B. subtilis biofilms in interaction with seeds and found cooperation in bacterial colonization of seed storage tissues and growth promotion. Combining confocal microscopy with fluorogenic probes, we found that two specific components of the extracellular matrix, amyloid protein TasA and fengycin, differentially increased the concentrations of reactive oxygen species inside seeds. Further, using electron and fluorescence microscopy and metabolomics, we showed that both TasA and fengycin targeted the oil bodies in the seed endosperm, resulting in specific changes in lipid metabolism and accumulation of glutathione-related molecules. In turn, this results in two different plant growth developmental programmes: TasA and fengycin stimulate the development of radicles, and fengycin alone stimulate the growth of adult plants and resistance in the phylloplane to the fungus Botrytis cinerea. Understanding mechanisms of bacterial growth promotion will enable the design of bespoke growth promotion strains.
- Published
- 2022
3. Mutualistic interactions between B. subtilis and seeds dictate plant development
- Author
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Berlanga-Clavero, M.V., primary, Molina-Santiago, C., additional, Caraballo-Rodríguez, A.M., additional, Petras, D., additional, Díaz-Martínez, L., additional, Pérez-García, A., additional, de Vicente, A., additional, Dorrestein, P. C., additional, and Romero, D., additional
- Published
- 2021
- Full Text
- View/download PDF
4. Operon
- Author
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Ramos, J.L., primary, García-Salamanca, A., additional, Molina-Santiago, C., additional, and Udaondo, Z., additional
- Published
- 2013
- Full Text
- View/download PDF
5. Antibiotic adjuvants: identification and clinical use
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Bernal, P, Molina-Santiago, C, Daddaoua, A, and Llamas, MA
- Subjects
MICROBIOLOGY ,Science & Technology ,MOLECULAR-MECHANISMS ,ANTIBACTERIAL ACTIVITY ,PSEUDOMONAS-AERUGINOSA ,BIOTECHNOLOGY & APPLIED MICROBIOLOGY ,MYCOBACTERIUM ,BETA-LACTAMASE INHIBITORS ,Bacterial Infections ,EFFICACY ,Microbiology ,Anti-Bacterial Agents ,COLISTIN COMBINATION ,Biotechnology & Applied Microbiology ,ESCHERICHIA-COLI ,Drug Resistance, Bacterial ,Humans ,MULTIDRUG-RESISTANCE ,GRAM-NEGATIVE BACTERIA ,Life Sciences & Biomedicine ,Adjuvants, Pharmaceutic ,0605 Microbiology - Published
- 2013
6. Unravelling the impact of environmental factors in shaping plant microbiomes.
- Author
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Pérez-Lorente AI, Romero D, and Molina-Santiago C
- Subjects
- Chenopodium quinoa microbiology, Malus microbiology, Plants microbiology, Stress, Physiological, Environment, Crops, Agricultural microbiology, Microbiota, Fungi genetics, Fungi physiology, Fungi classification, Bacteria genetics, Bacteria classification, Bacteria metabolism
- Abstract
This article emphasizes the significant role of environmental factors in shaping the plant microbiome, highlighting how bacterial and fungal communities influence plant responses to water stress, and how environmental factors shape fungal communities in crops. Furthermore, recent studies describe how different genotypes and levels of water stress affect the composition of bacterial communities associated with quinoa plants, as well as the relationship between environmental factors and the structure of fungal communities in apple fruit. These findings underscore the importance of understanding plant microbiome dynamics in developing effective crop protection strategies and improving agricultural sustainability with the objective of advance towards a microbiome-based strategy which allows us to improve crop tolerance to abiotic stresses., (© 2024 The Author(s). Microbial Biotechnology published by John Wiley & Sons Ltd.)
- Published
- 2024
- Full Text
- View/download PDF
7. microbeMASST: a taxonomically informed mass spectrometry search tool for microbial metabolomics data.
- Author
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Zuffa S, Schmid R, Bauermeister A, P Gomes PW, Caraballo-Rodriguez AM, El Abiead Y, Aron AT, Gentry EC, Zemlin J, Meehan MJ, Avalon NE, Cichewicz RH, Buzun E, Terrazas MC, Hsu CY, Oles R, Ayala AV, Zhao J, Chu H, Kuijpers MCM, Jackrel SL, Tugizimana F, Nephali LP, Dubery IA, Madala NE, Moreira EA, Costa-Lotufo LV, Lopes NP, Rezende-Teixeira P, Jimenez PC, Rimal B, Patterson AD, Traxler MF, Pessotti RC, Alvarado-Villalobos D, Tamayo-Castillo G, Chaverri P, Escudero-Leyva E, Quiros-Guerrero LM, Bory AJ, Joubert J, Rutz A, Wolfender JL, Allard PM, Sichert A, Pontrelli S, Pullman BS, Bandeira N, Gerwick WH, Gindro K, Massana-Codina J, Wagner BC, Forchhammer K, Petras D, Aiosa N, Garg N, Liebeke M, Bourceau P, Kang KB, Gadhavi H, de Carvalho LPS, Silva Dos Santos M, Pérez-Lorente AI, Molina-Santiago C, Romero D, Franke R, Brönstrup M, Vera Ponce de León A, Pope PB, La Rosa SL, La Barbera G, Roager HM, Laursen MF, Hammerle F, Siewert B, Peintner U, Licona-Cassani C, Rodriguez-Orduña L, Rampler E, Hildebrand F, Koellensperger G, Schoeny H, Hohenwallner K, Panzenboeck L, Gregor R, O'Neill EC, Roxborough ET, Odoi J, Bale NJ, Ding S, Sinninghe Damsté JS, Guan XL, Cui JJ, Ju KS, Silva DB, Silva FMR, da Silva GF, Koolen HHF, Grundmann C, Clement JA, Mohimani H, Broders K, McPhail KL, Ober-Singleton SE, Rath CM, McDonald D, Knight R, Wang M, and Dorrestein PC
- Subjects
- Humans, Databases, Factual, Tandem Mass Spectrometry, Metabolomics methods
- Abstract
microbeMASST, a taxonomically informed mass spectrometry (MS) search tool, tackles limited microbial metabolite annotation in untargeted metabolomics experiments. Leveraging a curated database of >60,000 microbial monocultures, users can search known and unknown MS/MS spectra and link them to their respective microbial producers via MS/MS fragmentation patterns. Identification of microbe-derived metabolites and relative producers without a priori knowledge will vastly enhance the understanding of microorganisms' role in ecology and human health., (© 2024. The Author(s).)
- Published
- 2024
- Full Text
- View/download PDF
8. A Taxonomically-informed Mass Spectrometry Search Tool for Microbial Metabolomics Data.
- Author
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Zuffa S, Schmid R, Bauermeister A, Gomes PWP, Caraballo-Rodriguez AM, Abiead YE, Aron AT, Gentry EC, Zemlin J, Meehan MJ, Avalon NE, Cichewicz RH, Buzun E, Terrazas MC, Hsu CY, Oles R, Ayala AV, Zhao J, Chu H, Kuijpers MCM, Jackrel SL, Tugizimana F, Nephali LP, Dubery IA, Madala NE, Moreira EA, Costa-Lotufo LV, Lopes NP, Rezende-Teixeira P, Jimenez PC, Rimal B, Patterson AD, Traxler MF, de Cassia Pessotti R, Alvarado-Villalobos D, Tamayo-Castillo G, Chaverri P, Escudero-Leyva E, Quiros-Guerrero LM, Bory AJ, Joubert J, Rutz A, Wolfender JL, Allard PM, Sichert A, Pontrelli S, Pullman BS, Bandeira N, Gerwick WH, Gindro K, Massana-Codina J, Wagner BC, Forchhammer K, Petras D, Aiosa N, Garg N, Liebeke M, Bourceau P, Kang KB, Gadhavi H, de Carvalho LPS, Dos Santos MS, Pérez-Lorente AI, Molina-Santiago C, Romero D, Franke R, Brönstrup M, de León AVP, Pope PB, Rosa SL, Barbera G, Roager HM, Laursen MF, Hammerle F, Siewert B, Peintner U, Licona-Cassani C, Rodriguez-Orduña L, Rampler E, Hildebrand F, Koellensperger G, Schoeny H, Hohenwallner K, Panzenboeck L, Gregor R, O'Neill EC, Roxborough ET, Odoi J, Bale NJ, Ding S, Sinninghe Damsté JS, Guan XL, Cui JJ, Ju KS, Silva DB, Silva FMR, da Silva GF, Koolen HHF, Grundmann C, Clement JA, Mohimani H, Broders K, McPhail KL, Ober-Singleton SE, Rath CM, McDonald D, Knight R, Wang M, and Dorrestein PC
- Abstract
MicrobeMASST, a taxonomically-informed mass spectrometry (MS) search tool, tackles limited microbial metabolite annotation in untargeted metabolomics experiments. Leveraging a curated database of >60,000 microbial monocultures, users can search known and unknown MS/MS spectra and link them to their respective microbial producers via MS/MS fragmentation patterns. Identification of microbial-derived metabolites and relative producers, without a priori knowledge, will vastly enhance the understanding of microorganisms' role in ecology and human health., Competing Interests: Disclosures PCD is an advisor to Cybele, consulted for MSD animal health in 2023, and he is a Co-founder and scientific advisor for Ometa Labs, Arome, and Enveda with prior approval by UC San Diego. MW is a Co-founder of Ometa labs. There are no known conflicts of interest in this work by the USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit. Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture.
- Published
- 2023
- Full Text
- View/download PDF
9. Nanotube-mediated plasmid transfer as a natural alternative for the improvement of industrially relevant bacteria.
- Author
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Molina-Santiago C and Bernal P
- Subjects
- Plasmids, DNA, Bacterial, Conjugation, Genetic, Bacteria genetics, Gene Transfer, Horizontal
- Published
- 2023
- Full Text
- View/download PDF
10. Sporulation Activated via σ W Protects Bacillus from a Tse1 Peptidoglycan Hydrolase Type VI Secretion System Effector.
- Author
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Pérez-Lorente AI, Molina-Santiago C, de Vicente A, and Romero D
- Abstract
Within bacterial communities, community members engage in interactions employing diverse offensive and defensive tools to reach coexistence. Extracellular-matrix production and sporulation are defensive mechanisms used by Bacillus subtilis cells when they interact with Pseudomonas chlororaphis strains expressing a type VI secretion system (T6SS). Here, we define Tse1 as the main toxin mobilized by the Pseudomonas chlororaphis T6SS that triggers sporulation in Bacillus subtilis. We characterize Tse1 as a peptidoglycan hydrolase that indirectly alters the dynamics and functionality of the Bacillus cell membrane. We also delineate the response of Bacillus cells to Tse1, which through the coordinated actions of the extracellular sigma factor σ
W and the cytoplasmic histidine kinases KinA and KinB, culminates in activation of the sporulation cascade. We propose that this cellular developmental response permits bacilli to defend against the toxicity of T6SS-mobilized Tse1 effector. IMPORTANCE The study of bacterial interactions is helping to define species-specific strategies used to modulate the competition dynamics underlying the development of community compositions. In this study, we deciphered the role of Pseudomonas T6SS when competing with Bacillus and the mechanism by which a T6SS-toxin modifies Bacillus physiology. We found that Pseudomonas triggers Bacillus sporulation by injecting through T6SS a toxin that we called Tse1. We found that Tse1 is a hydrolase that degrades Bacillus peptidoglycan and indirectly damages Bacillus membrane functionality. In addition, we demonstrated the mechanism by which Bacillus cells increase the sporulation rate upon recognition of the presence of Tse1. Interestingly, asporogenic Bacillus cells are more sensitive to T6SS activity, which led us to propose sporulation as a last resort of bacilli to overcome this family of toxins.- Published
- 2023
- Full Text
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11. A Noninvasive Method for Time-Lapse Imaging of Microbial Interactions and Colony Dynamics.
- Author
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Molina-Santiago C, Pearson JR, Berlanga-Clavero MV, Pérez-Lorente AI, de Vicente A, and Romero D
- Subjects
- Bacteria, Biofilms, Time-Lapse Imaging, Microbial Interactions, Microbiota
- Abstract
Complex interactions between microbial populations can greatly affect the overall properties of a microbial community, sometimes leading to cooperation and mutually beneficial coexistence, or competition and the death or displacement of organisms or subpopulations. Interactions between different biofilm populations are highly relevant in diverse scientific areas, from antimicrobial resistance to microbial ecology. The utilization of modern microscopic techniques has provided a new and interesting insight into how bacteria interact at the cellular level to form and maintain microbial biofilms. However, our ability to follow complex intraspecies and interspecies interactions in vivo at the microscopic level has remained somewhat limited. Here, we detailed BacLive, a novel noninvasive method for tracking bacterial growth and biofilm dynamics using high-resolution fluorescence microscopy and an associated ImageJ processing macro (https://github.com/BacLive) for easier data handling and image analysis. Finally, we provided examples of how BacLive can be used in the analysis of complex bacterial communities. IMPORTANCE Communication and interactions between single cells are continuously defining the structure and composition of microbial communities temporally and spatially. Methods routinely used to study these communities at the cellular level rely on sample manipulation which makes microscopic time-lapse experiments impossible. BacLive was conceived as a method for the noninvasive study of the formation and development of bacterial communities, such as biofilms, and the formation dynamics of specialized subpopulations in time-lapse experiments at a colony level. In addition, we developed a tool to simplify the processing and analysis of the data generated by this method.
- Published
- 2022
- Full Text
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12. Native metabolomics identifies the rivulariapeptolide family of protease inhibitors.
- Author
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Reher R, Aron AT, Fajtová P, Stincone P, Wagner B, Pérez-Lorente AI, Liu C, Shalom IYB, Bittremieux W, Wang M, Jeong K, Matos-Hernandez ML, Alexander KL, Caro-Diaz EJ, Naman CB, Scanlan JHW, Hochban PMM, Diederich WE, Molina-Santiago C, Romero D, Selim KA, Sass P, Brötz-Oesterhelt H, Hughes CC, Dorrestein PC, O'Donoghue AJ, Gerwick WH, and Petras D
- Subjects
- Chromatography, Liquid methods, Magnetic Resonance Spectroscopy methods, Tandem Mass Spectrometry methods, Metabolomics methods, Protease Inhibitors pharmacology
- Abstract
The identity and biological activity of most metabolites still remain unknown. A bottleneck in the exploration of metabolite structures and pharmaceutical activities is the compound purification needed for bioactivity assignments and downstream structure elucidation. To enable bioactivity-focused compound identification from complex mixtures, we develop a scalable native metabolomics approach that integrates non-targeted liquid chromatography tandem mass spectrometry and detection of protein binding via native mass spectrometry. A native metabolomics screen for protease inhibitors from an environmental cyanobacteria community reveals 30 chymotrypsin-binding cyclodepsipeptides. Guided by the native metabolomics results, we select and purify five of these compounds for full structure elucidation via tandem mass spectrometry, chemical derivatization, and nuclear magnetic resonance spectroscopy as well as evaluation of their biological activities. These results identify rivulariapeptolides as a family of serine protease inhibitors with nanomolar potency, highlighting native metabolomics as a promising approach for drug discovery, chemical ecology, and chemical biology studies., (© 2022. The Author(s).)
- Published
- 2022
- Full Text
- View/download PDF
13. Mechanisms of resistance to glyphosate: an example of bacterial adaptability to anthropogenic substances.
- Author
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Molina-Santiago C and Udaondo Z
- Subjects
- Bacteria genetics, Glyphosate, Glycine analogs & derivatives, Glycine pharmacology, Herbicides pharmacology
- Published
- 2022
- Full Text
- View/download PDF
14. GNPS Dashboard: collaborative exploration of mass spectrometry data in the web browser.
- Author
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Petras D, Phelan VV, Acharya D, Allen AE, Aron AT, Bandeira N, Bowen BP, Belle-Oudry D, Boecker S, Cummings DA Jr, Deutsch JM, Fahy E, Garg N, Gregor R, Handelsman J, Navarro-Hoyos M, Jarmusch AK, Jarmusch SA, Louie K, Maloney KN, Marty MT, Meijler MM, Mizrahi I, Neve RL, Northen TR, Molina-Santiago C, Panitchpakdi M, Pullman B, Puri AW, Schmid R, Subramaniam S, Thukral M, Vasquez-Castro F, Dorrestein PC, and Wang M
- Subjects
- Data Visualization, Mass Spectrometry, Software, Web Browser
- Published
- 2022
- Full Text
- View/download PDF
15. Chemical Proportionality within Molecular Networks.
- Author
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Petras D, Caraballo-Rodríguez AM, Jarmusch AK, Molina-Santiago C, Gauglitz JM, Gentry EC, Belda-Ferre P, Romero D, Tsunoda SM, Dorrestein PC, and Wang M
- Subjects
- Humans, Workflow, Biological Products, Tandem Mass Spectrometry
- Abstract
Molecular networking of non-targeted tandem mass spectrometry data connects structurally related molecules based on similar fragmentation spectra. Here, we report the Chem ical Pro portionality (ChemProp) contextualization of molecular networks. ChemProp scores the changes of abundance between two connected nodes over sequential data series (e.g., temporal or spatial relationships), which can be displayed as a direction within the network to prioritize potential biological and chemical transformations or proportional changes of (biosynthetically) related compounds. We tested the ChemProp workflow on a ground truth data set of a defined mixture and highlighted the utility of the tool to prioritize specific molecules within biological samples, including bacterial transformations of bile acids, human drug metabolism, and bacterial natural products biosynthesis. The ChemProp workflow is freely available through the Global Natural Products Social Molecular Networking (GNPS) environment.
- Published
- 2021
- Full Text
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16. Chemical interplay and complementary adaptative strategies toggle bacterial antagonism and co-existence.
- Author
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Molina-Santiago C, Vela-Corcía D, Petras D, Díaz-Martínez L, Pérez-Lorente AI, Sopeña-Torres S, Pearson J, Caraballo-Rodríguez AM, Dorrestein PC, de Vicente A, and Romero D
- Subjects
- Alleles, Anti-Infective Agents pharmacology, Bacillus drug effects, Bacterial Proteins genetics, Bacterial Proteins metabolism, Drug Resistance, Bacterial drug effects, Microbial Sensitivity Tests, Mutation genetics, Permeability, Pseudomonas drug effects, Pseudomonas growth & development, Adaptation, Physiological drug effects, Bacillus physiology, Pseudomonas physiology
- Abstract
Bacterial communities are in a continuous adaptive and evolutionary race for survival. In this work we expand our knowledge on the chemical interplay and specific mutations that modulate the transition from antagonism to co-existence between two plant-beneficial bacteria, Pseudomonas chlororaphis PCL1606 and Bacillus amyloliquefaciens FZB42. We reveal that the bacteriostatic activity of bacillaene produced by Bacillus relies on an interaction with the protein elongation factor FusA of P. chlororaphis and how mutations in this protein lead to tolerance to bacillaene and other protein translation inhibitors. Additionally, we describe how the unspecific tolerance of B. amyloliquefaciens to antimicrobials associated with mutations in the glycerol kinase GlpK is provoked by a decrease of Bacillus cell membrane permeability, among other pleiotropic responses. We conclude that nutrient specialization and mutations in basic biological functions are bacterial adaptive dynamics that lead to the coexistence of two primary competitive bacterial species rather than their mutual eradication., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2021 The Author(s). Published by Elsevier Inc. All rights reserved.)
- Published
- 2021
- Full Text
- View/download PDF
17. Bacterial extracellular matrix as a natural source of biotechnologically multivalent materials.
- Author
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Molina-Santiago C, de Vicente A, and Romero D
- Abstract
The extracellular matrix (ECM) is an intricate megastructure made by bacterial cells to form architecturally complex biostructures called biofilms. Protection of cells, modulation of cell-to-cell signalling, cell differentiation and environmental sensing are functions of the ECM that reflect its diverse chemical composition. Proteins, polysaccharides and eDNA have specific functionalities while cooperatively interacting to sustain the architecture and biological relevance of the ECM. The accumulated evidence on the chemical heterogeneity and specific functionalities of ECM components has attracted attention because of their potential biotechnological applications, from agriculture to the water and food industries. This review compiles information on the most relevant bacterial ECM components, the biophysical and chemical features responsible for their biological roles, and their potential to be further translated into biotechnological applications., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2021 Published by Elsevier B.V. on behalf of Research Network of Computational and Structural Biotechnology.)
- Published
- 2021
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18. A community resource for paired genomic and metabolomic data mining.
- Author
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Schorn MA, Verhoeven S, Ridder L, Huber F, Acharya DD, Aksenov AA, Aleti G, Moghaddam JA, Aron AT, Aziz S, Bauermeister A, Bauman KD, Baunach M, Beemelmanns C, Beman JM, Berlanga-Clavero MV, Blacutt AA, Bode HB, Boullie A, Brejnrod A, Bugni TS, Calteau A, Cao L, Carrión VJ, Castelo-Branco R, Chanana S, Chase AB, Chevrette MG, Costa-Lotufo LV, Crawford JM, Currie CR, Cuypers B, Dang T, de Rond T, Demko AM, Dittmann E, Du C, Drozd C, Dujardin JC, Dutton RJ, Edlund A, Fewer DP, Garg N, Gauglitz JM, Gentry EC, Gerwick L, Glukhov E, Gross H, Gugger M, Guillén Matus DG, Helfrich EJN, Hempel BF, Hur JS, Iorio M, Jensen PR, Kang KB, Kaysser L, Kelleher NL, Kim CS, Kim KH, Koester I, König GM, Leao T, Lee SR, Lee YY, Li X, Little JC, Maloney KN, Männle D, Martin H C, McAvoy AC, Metcalf WW, Mohimani H, Molina-Santiago C, Moore BS, Mullowney MW, Muskat M, Nothias LF, O'Neill EC, Parkinson EI, Petras D, Piel J, Pierce EC, Pires K, Reher R, Romero D, Roper MC, Rust M, Saad H, Saenz C, Sanchez LM, Sørensen SJ, Sosio M, Süssmuth RD, Sweeney D, Tahlan K, Thomson RJ, Tobias NJ, Trindade-Silva AE, van Wezel GP, Wang M, Weldon KC, Zhang F, Ziemert N, Duncan KR, Crüsemann M, Rogers S, Dorrestein PC, Medema MH, and van der Hooft JJJ
- Subjects
- Databases, Factual, Data Mining methods, Genomics methods, Metabolomics methods
- Published
- 2021
- Full Text
- View/download PDF
19. More than words: the chemistry behind the interactions in the plant holobiont.
- Author
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Berlanga-Clavero MV, Molina-Santiago C, de Vicente A, and Romero D
- Subjects
- Germination physiology, Microbial Interactions physiology, Microbiota physiology, Plant Roots microbiology, Plants metabolism, Rhizosphere, Seeds growth & development, Seeds microbiology, Signal Transduction physiology, Virulence Factors metabolism, Bacteria metabolism, Plant Development physiology, Plants microbiology, Symbiosis physiology
- Abstract
Plants and microbes have evolved sophisticated ways to communicate and coexist. The simplest interactions that occur in plant-associated habitats, i.e., those involved in disease detection, depend on the production of microbial pathogenic and virulence factors and the host's evolved immunological response. In contrast, microbes can also be beneficial for their host plants in a number of ways, including fighting pathogens and promoting plant growth. In order to clarify the mechanisms directly involved in these various plant-microbe interactions, we must still deepen our understanding of how these interkingdom communication systems, which are constantly modulated by resident microbial activity, are established and, most importantly, how their effects can span physically separated plant compartments. Efforts in this direction have revealed a complex and interconnected network of molecules and associated metabolic pathways that modulate plant-microbe and microbe-microbe communication pathways to regulate diverse ecological responses. Once sufficiently understood, these pathways will be biotechnologically exploitable, for example, in the use of beneficial microbes in sustainable agriculture. The aim of this review is to present the latest findings on the dazzlingly diverse arsenal of molecules that efficiently mediate specific microbe-microbe and microbe-plant communication pathways during plant development and on different plant organs., (© 2020 Society for Applied Microbiology and John Wiley & Sons Ltd.)
- Published
- 2020
- Full Text
- View/download PDF
20. Chemical fertilization: a short-term solution for plant productivity?
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Molina-Santiago C and Matilla MA
- Subjects
- Fertilization, Plants, Soil Microbiology
- Abstract
The effect of long-term chemical fertilization on plant-microorganisms and microbe-microbe interactions., (© 2019 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.)
- Published
- 2020
- Full Text
- View/download PDF
21. Dual functionality of the amyloid protein TasA in Bacillus physiology and fitness on the phylloplane.
- Author
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Cámara-Almirón J, Navarro Y, Díaz-Martínez L, Magno-Pérez-Bryan MC, Molina-Santiago C, Pearson JR, de Vicente A, Pérez-García A, and Romero D
- Subjects
- Amyloidogenic Proteins genetics, Bacillus subtilis metabolism, Bacterial Adhesion, Bacterial Proteins genetics, Biofilms, Cell Death, Cell Membrane metabolism, Cucurbitaceae microbiology, Ecology, Lipopeptides, Mutation, Transcriptome, Amyloidogenic Proteins metabolism, Bacillus physiology, Bacterial Proteins metabolism
- Abstract
Bacteria can form biofilms that consist of multicellular communities embedded in an extracellular matrix (ECM). In Bacillus subtilis, the main protein component of the ECM is the functional amyloid TasA. Here, we study further the roles played by TasA in B. subtilis physiology and biofilm formation on plant leaves and in vitro. We show that ΔtasA cells exhibit a range of cytological symptoms indicative of excessive cellular stress leading to increased cell death. TasA associates to the detergent-resistant fraction of the cell membrane, and the distribution of the flotillin-like protein FloT is altered in ΔtasA cells. We propose that, in addition to a structural function during ECM assembly and interactions with plants, TasA contributes to the stabilization of membrane dynamics as cells enter stationary phase.
- Published
- 2020
- Full Text
- View/download PDF
22. Untargeted mass spectrometry-based metabolomics approach unveils molecular changes in raw and processed foods and beverages.
- Author
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Gauglitz JM, Aceves CM, Aksenov AA, Aleti G, Almaliti J, Bouslimani A, Brown EA, Campeau A, Caraballo-Rodríguez AM, Chaar R, da Silva RR, Demko AM, Di Ottavio F, Elijah E, Ernst M, Ferguson LP, Holmes X, Jarmusch AK, Jiang L, Kang KB, Koester I, Kwan B, Li J, Li Y, Melnik AV, Molina-Santiago C, Ni B, Oom AL, Panitchpakdi MW, Petras D, Quinn R, Sikora N, Spengler K, Teke B, Tripathi A, Ul-Hasan S, van der Hooft JJJ, Vargas F, Vrbanac A, Vu AQ, Wang SC, Weldon K, Wilson K, Wozniak JM, Yoon M, Bandeira N, and Dorrestein PC
- Subjects
- Fermentation, Workflow, Beverages analysis, Food Analysis, Food Handling, Mass Spectrometry, Metabolomics
- Abstract
In our daily lives, we consume foods that have been transported, stored, prepared, cooked, or otherwise processed by ourselves or others. Food storage and preparation have drastic effects on the chemical composition of foods. Untargeted mass spectrometry analysis of food samples has the potential to increase our chemical understanding of these processes by detecting a broad spectrum of chemicals. We performed a time-based analysis of the chemical changes in foods during common preparations, such as fermentation, brewing, and ripening, using untargeted mass spectrometry and molecular networking. The data analysis workflow presented implements an approach to study changes in food chemistry that can reveal global alterations in chemical profiles, identify changes in abundance, as well as identify specific chemicals and their transformation products. The data generated in this study are publicly available, enabling the replication and re-analysis of these data in isolation, and serve as a baseline dataset for future investigations., (Copyright © 2019 Elsevier Ltd. All rights reserved.)
- Published
- 2020
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- View/download PDF
23. Microbiomes as the new keystone for life sciences development.
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Udaondo Z and Molina-Santiago C
- Subjects
- Animals, Humans, Biological Science Disciplines methods, Biological Science Disciplines trends, Microbiota
- Published
- 2019
- Full Text
- View/download PDF
24. The extracellular matrix protects Bacillus subtilis colonies from Pseudomonas invasion and modulates plant co-colonization.
- Author
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Molina-Santiago C, Pearson JR, Navarro Y, Berlanga-Clavero MV, Caraballo-Rodriguez AM, Petras D, García-Martín ML, Lamon G, Haberstein B, Cazorla FM, de Vicente A, Loquet A, Dorrestein PC, and Romero D
- Subjects
- Bacillus subtilis growth & development, Bacillus subtilis metabolism, Bacterial Proteins genetics, Bacterial Proteins metabolism, Colony Count, Microbial, Phosphotransferases genetics, Phosphotransferases metabolism, Plant Leaves microbiology, Protein Kinases genetics, Protein Kinases metabolism, Pseudomonas chlororaphis growth & development, Pseudomonas chlororaphis metabolism, Seeds microbiology, Spores, Bacterial genetics, Spores, Bacterial growth & development, Spores, Bacterial metabolism, Symbiosis physiology, Type VI Secretion Systems genetics, Type VI Secretion Systems metabolism, Bacillus subtilis genetics, Cucurbitaceae microbiology, Extracellular Matrix metabolism, Gene Expression Regulation, Bacterial, Microbial Interactions genetics, Pseudomonas chlororaphis genetics
- Abstract
Bacteria of the genera Pseudomonas and Bacillus can promote plant growth and protect plants from pathogens. However, the interactions between these plant-beneficial bacteria are understudied. Here, we explore the interaction between Bacillus subtilis 3610 and Pseudomonas chlororaphis PCL1606. We show that the extracellular matrix protects B. subtilis colonies from infiltration by P. chlororaphis. The absence of extracellular matrix results in increased fluidity and loss of structure of the B. subtilis colony. The P. chlororaphis type VI secretion system (T6SS) is activated upon contact with B. subtilis cells, and stimulates B. subtilis sporulation. Furthermore, we find that B. subtilis sporulation observed prior to direct contact with P. chlororaphis is mediated by histidine kinases KinA and KinB. Finally, we demonstrate the importance of the extracellular matrix and the T6SS in modulating the coexistence of the two species on melon plant leaves and seeds.
- Published
- 2019
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25. The race for antimicrobials in the multidrug resistance era.
- Author
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Molina-Santiago C, de Vicente A, and Romero D
- Subjects
- Bacteria genetics, Bacteria metabolism, Bacterial Infections drug therapy, Drug Discovery, Humans, Anti-Bacterial Agents pharmacology, Bacteria drug effects, Bacterial Infections microbiology, Drug Resistance, Multiple, Bacterial
- Abstract
The appearance of multidrug-resistant pathogens is a major threat to human health with the reemergence of fatal and untreatable diseases. In addition to a rational use of the well-known and available antibiotics, two complementary ways to overcome this public health issue are (i) the discovery of new antimicrobials and (ii) the chemical modification of pre-existing potent antibiotics. In this article, we highlight some of the strategies to generate new and promising antimicrobials for use in the management of these so-called 'superbugs'., (© 2017 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.)
- Published
- 2018
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26. Insights in a novel gram-positive type IV secretion system.
- Author
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Molina-Santiago C
- Published
- 2018
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27. Ruminal metagenomic libraries as a source of relevant hemicellulolytic enzymes for biofuel production.
- Author
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Duque E, Daddaoua A, Cordero BF, Udaondo Z, Molina-Santiago C, Roca A, Solano J, Molina-Alcaide E, Segura A, and Ramos JL
- Subjects
- Animals, Bacteria chemistry, Bacteria genetics, Bacteria isolation & purification, Bacterial Proteins chemistry, Bacterial Proteins genetics, Cattle, Cloning, Molecular, Endo-1,4-beta Xylanases chemistry, Endo-1,4-beta Xylanases genetics, Endo-1,4-beta Xylanases metabolism, Enzyme Stability, Glycoside Hydrolases chemistry, Glycoside Hydrolases genetics, Metagenomics, Open Reading Frames, Polysaccharides metabolism, Saccharum chemistry, Saccharum metabolism, Bacteria enzymology, Bacterial Proteins metabolism, Biofuels analysis, Glycoside Hydrolases metabolism, Rumen microbiology
- Abstract
The success of second-generation (2G) ethanol technology relies on the efficient transformation of hemicellulose into monosaccharides and, particularly, on the full conversion of xylans into xylose for over 18% of fermentable sugars. We sought new hemicellulases using ruminal liquid, after enrichment of microbes with industrial lignocellulosic substrates and preparation of metagenomic libraries. Among 150 000 fosmid clones tested, we identified 22 clones with endoxylanase activity and 125 with β-xylosidase activity. These positive clones were sequenced en masse, and the analysis revealed open reading frames with a low degree of similarity with known glycosyl hydrolases families. Among them, we searched for enzymes that were thermostable (activity at > 50°C) and that operate at high rate at pH around 5. Upon a wide series of assays, the clones exhibiting the highest endoxylanase and β-xylosidase activities were identified. The fosmids were sequenced, and the corresponding genes cloned, expressed and proteins purified. We found that the activity of the most active β-xylosidase was at least 10-fold higher than that in commercial enzymatic fungal cocktails. Endoxylanase activity was in the range of fungal enzymes. Fungal enzymatic cocktails supplemented with the bacterial hemicellulases exhibited enhanced release of sugars from pretreated sugar cane straw, a relevant agricultural residue., (© 2018 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.)
- Published
- 2018
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28. Interspecies cross-talk between co-cultured Pseudomonas putida and Escherichia coli.
- Author
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Molina-Santiago C, Udaondo Z, Cordero BF, and Ramos JL
- Subjects
- Bacterial Proteins genetics, Bacterial Proteins metabolism, Escherichia coli classification, Escherichia coli genetics, Escherichia coli isolation & purification, Food Microbiology, Pseudomonas putida classification, Pseudomonas putida genetics, Pseudomonas putida isolation & purification, Soil Microbiology, Escherichia coli physiology, Pseudomonas putida physiology
- Abstract
Pseudomonas putida and Escherichia coli are ubiquitous microorganisms that can be isolated from soil rhizosphere, the surface of vegetables, fresh waters and wastewaters - environments in which they likely co-exist. Despite this, the potential interactions between these microbes have not been studied in detail. To analyse these interactions, we carried out RNA-seq transcriptomic analysis of these microbes as monocultures and as co-cultures. Our results show that co-culture of these microbes significantly alters transcriptional profiles. The most dramatic transcriptional changes in both microorganisms were involved in central carbon metabolism, as well as adhesion to surfaces and the activation of drug efflux pumps. We also found that acetate production was one of the mechanisms used by E. coli K-12 MG1655 in response to the presence of P. putida DOT-T1E., (© 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.)
- Published
- 2017
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29. Global transcriptional response of solvent-sensitive and solvent-tolerant Pseudomonas putida strains exposed to toluene.
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Molina-Santiago C, Udaondo Z, Gómez-Lozano M, Molin S, and Ramos JL
- Subjects
- Bacterial Proteins genetics, Bacterial Proteins metabolism, Biodegradation, Environmental, Pseudomonas putida genetics, Gene Expression Regulation, Bacterial physiology, Pseudomonas putida drug effects, Pseudomonas putida metabolism, Solvents pharmacology, Toluene pharmacology, Transcriptome
- Abstract
Pseudomonas putida strains are generally recognized as solvent tolerant, exhibiting varied sensitivity to organic solvents. Pan-genome analysis has revealed that 30% of genes belong to the core-genome of Pseudomonas. Accessory and unique genes confer high degree of adaptability and capabilities for the degradation and synthesis of a wide range of chemicals. For the use of these microbes in bioremediation and biocatalysis, it is critical to understand the mechanisms underlying these phenotypic differences. In this study, RNA-seq analysis compared the short- and long-term responses of the toluene-sensitive KT2440 strain and the highly tolerant DOT-T1E strain. The sensitive strain activates a larger number of genes in a higher magnitude than DOT-T1E. This is expected because KT2440 bears one toluene tolerant pump, while DOT-T1E encodes three of these pumps. Both strains activate membrane modifications to reduce toluene membrane permeability. The KT2440 strain activates the TCA cycle to generate energy, while avoiding energy-intensive processes such as flagellar biosynthesis. This suggests that KT2440 responds to toluene by focusing on survival mechanisms. The DOT-T1E strain activates toluene degradation pathways, using toluene as source of energy. Among the unique genes encoded by DOT-T1E is a 70 kb island composed of genes of unknown function induced in response to toluene., (© 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.)
- Published
- 2017
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30. Pseudomonas putida as a platform for the synthesis of aromatic compounds.
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Molina-Santiago C, Cordero BF, Daddaoua A, Udaondo Z, Manzano J, Valdivia M, Segura A, Ramos JL, and Duque E
- Subjects
- Bacterial Proteins genetics, Bacterial Proteins metabolism, Industrial Microbiology, Pseudomonas putida genetics, Cinnamates metabolism, Flavoring Agents metabolism, Phenylalanine biosynthesis, Phenylethyl Alcohol metabolism, Pseudomonas putida metabolism
- Abstract
Aromatic compounds such as l-phenylalanine, 2-phenylethanol and trans-cinnamate are aromatic compounds of industrial interest. Current trends support replacement of chemical synthesis of these compounds by 'green' alternatives produced in microbial cell factories. The solvent-tolerant Pseudomonas putida DOT-T1E strain was genetically modified to produce up to 1 g l-1 of l-phenylalanine. In order to engineer this strain, we carried out the following stepwise process: (1) we selected random mutants that are resistant to toxic phenylalanine analogues; (2) we then deleted up to five genes belonging to phenylalanine metabolism pathways, which greatly diminished the internal metabolism of phenylalanine; and (3) in these mutants, we overexpressed the pheAfbr gene, which encodes a recombinant variant of PheA that is insensitive to feedback inhibition by phenylalanine. Furthermore, by introducing new genes, we were able to further extend the diversity of compounds produced. Introduction of histidinol phosphate transferase (PP_0967), phenylpyruvate decarboxylase (kdc) and an alcohol dehydrogenase (adh) enabled the strain to produce up to 180 mg l-1 2-phenylethanol. When phenylalanine ammonia lyase (pal) was introduced, the resulting strain produced up to 200 mg l-1 of trans-cinnamate. These results demonstrate that P. putida can serve as a promising microbial cell factory for the production of l-phenylalanine and related compounds.
- Published
- 2016
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31. A Pseudomonas putida double mutant deficient in butanol assimilation: a promising step for engineering a biological biofuel production platform.
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Cuenca Mdel S, Molina-Santiago C, Gómez-García MR, and Ramos JL
- Subjects
- DNA Transposable Elements genetics, Histidine Kinase, Malate Synthase genetics, Mutagenesis, Insertional, Protein Kinases genetics, Biofuels microbiology, Butanols metabolism, Genetic Engineering methods, Pseudomonas putida genetics, Pseudomonas putida metabolism
- Abstract
Biological production in heterologous hosts is of interest for the production of the C4 alcohol (butanol) and other chemicals. However, some hurdles need to be overcome in order to achieve an economically viable process; these include avoiding the consumption of butanol and maintaining tolerance to this solvent during production. Pseudomonas putida is a potential host for solvent production; in order to further adapt P. putida to this role, we generated mini-Tn5 mutant libraries in strain BIRD-1 that do not consume butanol. We analyzed the insertion site of the mini-Tn5 in a mutant that was deficient in assimilation of butanol using arbitrary PCR followed by Sanger sequencing and found that the transposon was inserted in the malate synthase B gene. Here, we show that in a second round of mutagenesis a double mutant unable to take up butanol had an insertion in a gene coding for a multisensor hybrid histidine kinase. The genetic context of the histidine kinase sensor revealed the presence of a set of genes potentially involved in butanol assimilation; qRT-PCR analysis showed induction of this set of genes in the wild type and the malate synthase mutant but not in the double mutant., (© FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)
- Published
- 2016
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32. Understanding butanol tolerance and assimilation in Pseudomonas putida BIRD-1: an integrated omics approach.
- Author
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Cuenca Mdel S, Roca A, Molina-Santiago C, Duque E, Armengaud J, Gómez-Garcia MR, and Ramos JL
- Subjects
- Acetate-CoA Ligase genetics, Acetate-CoA Ligase metabolism, Acyl-CoA Dehydrogenases genetics, Acyl-CoA Dehydrogenases metabolism, Bacterial Proteins genetics, Bacterial Proteins metabolism, Proteomics, Pseudomonas putida enzymology, Pseudomonas putida genetics, Butanols metabolism, Pseudomonas putida metabolism
- Abstract
Pseudomonas putida BIRD-1 has the potential to be used for the industrial production of butanol due to its solvent tolerance and ability to metabolize low-cost compounds. However, the strain has two major limitations: it assimilates butanol as sole carbon source and butanol concentrations above 1% (v/v) are toxic. With the aim of facilitating BIRD-1 strain design for industrial use, a genome-wide mini-Tn5 transposon mutant library was screened for clones exhibiting increased butanol sensitivity or deficiency in butanol assimilation. Twenty-one mutants were selected that were affected in one or both of the processes. These mutants exhibited insertions in various genes, including those involved in the TCA cycle, fatty acid metabolism, transcription, cofactor synthesis and membrane integrity. An omics-based analysis revealed key genes involved in the butanol response. Transcriptomic and proteomic studies were carried out to compare short and long-term tolerance and assimilation traits. Pseudomonas putida initiates various butanol assimilation pathways via alcohol and aldehyde dehydrogenases that channel the compound to central metabolism through the glyoxylate shunt pathway. Accordingly, isocitrate lyase - a key enzyme of the pathway - was the most abundant protein when butanol was used as the sole carbon source. Upregulation of two genes encoding proteins PPUBIRD1_2240 and PPUBIRD1_2241 (acyl-CoA dehydrogenase and acyl-CoA synthetase respectively) linked butanol assimilation with acyl-CoA metabolism. Butanol tolerance was found to be primarily linked to classic solvent defense mechanisms, such as efflux pumps, membrane modifications and control of redox state. Our results also highlight the intensive energy requirements for butanol production and tolerance; thus, enhancing TCA cycle operation may represent a promising strategy for enhanced butanol production., (© 2015 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.)
- Published
- 2016
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33. Differential transcriptional response to antibiotics by Pseudomonas putida DOT-T1E.
- Author
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Molina-Santiago C, Daddaoua A, Gómez-Lozano M, Udaondo Z, Molin S, and Ramos JL
- Subjects
- Pseudomonas putida genetics, RNA, Messenger genetics, Solvents pharmacology, Anti-Bacterial Agents pharmacology, Drug Resistance, Multiple, Bacterial genetics, Pseudomonas putida drug effects, RNA, Small Untranslated genetics, Transcription, Genetic drug effects
- Abstract
Multi-drug resistant bacteria are a major threat to humanity, especially because the current battery of known antibiotics is not sufficient to combat infections produced by these microbes. Therefore, the study of how current antibiotics act and how bacteria defend themselves against antibiotics is of critical importance. Pseudomonas putida DOT-T1E exhibits an impressive array of RND efflux pumps, which confer this microorganism high resistance to organic solvents and antibiotics that would kill most other microorganisms. We have chosen DOT-T1E as a model microbe to study the microbial responses to a wide battery of antibiotics (chloramphenicol, rifampicin, tetracycline, ciprofloxacin, ampicillin, kanamycin, spectinomycin and gentamicin). Ribonucleic acid sequencing (RNA)-seq analyses revealed that each antibiotic provokes a unique transcriptional response profile in DOT-T1E. While many of the genes identified were related to known antibiotic targets, others were unrelated or encoded hypothetical proteins. These results indicate that our knowledge of antibiotic resistance mechanisms is still partial. We also identified 138 new small RNAs (sRNAs) in DOT-T1E, dramatically adding to the 16 that have been previously described. Importantly, our results reveal that a correlation exists between the expression of messenger RNA and sRNA, indicating that some of these sRNAs are likely involved in fine tuning the expression of antibiotic resistance genes. Taken together, these findings open new frontiers in the fight against multi-drug resistant bacteria and point to the potential use of sRNAs as novel antimicrobial targets., (© 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.)
- Published
- 2015
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34. Efflux pump-deficient mutants as a platform to search for microbes that produce antibiotics.
- Author
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Molina-Santiago C, Udaondo Z, Daddaoua A, Roca A, Martín J, Pérez-Victoria I, Reyes F, and Ramos JL
- Subjects
- Anti-Bacterial Agents isolation & purification, Bacillus, Bacteria isolation & purification, Biological Transport, Active, Drug Synergism, Fungi, Humans, Microbial Sensitivity Tests, Pseudomonas genetics, Pseudomonas growth & development, Anti-Bacterial Agents metabolism, Antibiosis, Bacteria metabolism, Environmental Microbiology, Membrane Transport Proteins deficiency, Pseudomonas drug effects
- Abstract
Pseudomonas putida DOT-T1E-18 is a strain deficient in the major antibiotic efflux pump (TtgABC) that exhibits an overall increased susceptibility to a wide range of drugs when compared with the wild-type strain. We used this strain as a platform to search for microbes able to produce antibiotics that inhibit growth. A collection of 2400 isolates from soil, sediments and water was generated and a drop assay developed to identify, via growth inhibition halos, strains that prevent the growth of DOT-T1E-18 on solid Luria-Bertani plates. In this study, 35 different isolates that produced known and unknown antibiotics were identified. The most potent inhibitor of DOT-T1E-18 growth was an isolate named 250J that, through multi-locus sequence analysis, was identified as a Pseudomonas sp. strain. Culture supernatants of 250J contain four different xantholysins that prevent growth of Gram-positive bacteria, Gram-negative and fungi. Two of the xantholysins were produced in higher concentrations and purified. Xantholysin A was effective against Bacillus, Lysinibacillus and Rhodococcus strains, and the effect against these microbes was enhanced when used in combination with other antibiotics such as ampicillin, gentamicin and kanamycin. Xantholysin C was also efficient against Gram-positive bacteria and showed an interesting antimicrobial effect against Pseudomonas strains, and a synergistic inhibitory effect with ampicillin, chloramphenicol and gentamicin., (© 2015 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.)
- Published
- 2015
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35. Mechanisms of solvent resistance mediated by interplay of cellular factors in Pseudomonas putida.
- Author
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Ramos JL, Sol Cuenca M, Molina-Santiago C, Segura A, Duque E, Gómez-García MR, Udaondo Z, and Roca A
- Subjects
- Genes, Bacterial genetics, Pseudomonas putida genetics, RNA, Small Untranslated metabolism, Drug Resistance, Bacterial genetics, Pseudomonas putida drug effects, Pseudomonas putida physiology, Solvents toxicity
- Abstract
A number of microorganisms have the ability to thrive in the presence of a range of toxic solvents. Tolerance to these chemicals is a multifactorial process, meaning that bacterial cells use a set of physiological and gene expression changes to overcome the damage imparted by these chemicals. This review focuses mainly on issues related to tolerance to aromatic hydrocarbons and butanol in Pseudomonas, although other microorganisms are also discussed. Pseudomonas putida strains contain a circular chromosome of approximately 6 Mbp which encodes about 5300 genes. A combination of physiological and biochemical assays, a genome-wide collection of mutants and several omics approaches have provided useful information to help identify functions involved in solvent tolerance in P. putida. The solvent response involves fine-tuning of lipid fluidity to adjust membrane functions including impermeabilization, activation of a general stress-response system, increased energy generation and induction of specific efflux pumps that extrude solvents to the medium. These responses are modulated at the transcriptional level by local and global regulators as well as by a number of sRNAs whose levels fluctuate with the presence of solvents in the environment. Taken as a whole these regulatory inputs orchestrate the complex network of metabolic responses observed after solvent addition., (© FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)
- Published
- 2015
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36. Draft whole-genome sequence of the antibiotic-producing soil isolate Pseudomonas sp. strain 250J.
- Author
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Molina-Santiago C, Udaondo Z, and Ramos JL
- Subjects
- Depsipeptides metabolism, Metabolic Networks and Pathways genetics, Molecular Sequence Data, Phenylacetates metabolism, Pseudomonas isolation & purification, Soil Microbiology, Anti-Bacterial Agents metabolism, DNA, Bacterial chemistry, DNA, Bacterial genetics, Genome, Bacterial, Pseudomonas genetics, Pseudomonas metabolism, Sequence Analysis, DNA
- Abstract
Bacteria of the genus Pseudomonas are becoming increasing well known for their ability to produce a wide range of antimicrobial compounds. In a large-scale screening for antibiotic producers, we identified a soil isolate that uses 4-hydroxyphenylacetate as the sole carbon source, Pseudomonas sp. strain 250J, which produces cyclic lipodepsipeptides of the xantholysin family during the stationary phase of growth. The closest relatives of this strain are Pseudomonas mosselii, Pseudomonas soli and Pseudomonas entomophila. Sequencing of the 250J genome allowed us to find the genes relevant to antibiotic production, those which allow utilization of 4-hydroxyphenylacetate as a sole carbon source and a set of genes potentially involved in biocontrol., (© 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.)
- Published
- 2015
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37. Diversity of small RNAs expressed in Pseudomonas species.
- Author
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Gómez-Lozano M, Marvig RL, Molina-Santiago C, Tribelli PM, Ramos JL, and Molin S
- Subjects
- Conserved Sequence, Gene Expression Profiling, Genetic Variation, Pseudomonas classification, RNA, Bacterial analysis, RNA, Small Untranslated analysis, Sequence Homology, Nucleic Acid, Pseudomonas genetics, RNA, Bacterial genetics, RNA, Small Untranslated genetics
- 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., (© 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.)
- Published
- 2015
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38. GtrS and GltR form a two-component system: the central role of 2-ketogluconate in the expression of exotoxin A and glucose catabolic enzymes in Pseudomonas aeruginosa.
- Author
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Daddaoua A, Molina-Santiago C, de la Torre J, Krell T, and Ramos JL
- Subjects
- ADP Ribose Transferases metabolism, Bacterial Proteins chemistry, Bacterial Toxins metabolism, Binding Sites, Exotoxins metabolism, Promoter Regions, Genetic, Protein Structure, Tertiary, Pseudomonas aeruginosa enzymology, Pseudomonas aeruginosa metabolism, Repressor Proteins metabolism, Transcriptional Activation, Virulence Factors metabolism, Pseudomonas aeruginosa Exotoxin A, ADP Ribose Transferases genetics, Bacterial Proteins metabolism, Bacterial Toxins genetics, Exotoxins genetics, Gene Expression Regulation, Bacterial, Gluconates metabolism, Glucose metabolism, Monosaccharide Transport Proteins metabolism, Protein Kinases metabolism, Pseudomonas aeruginosa genetics, Virulence Factors genetics
- Abstract
In the human pathogen Pseudomonas aeruginosa, the GltR regulator is required for glucose transport, whereas GtrS is a sensor kinase that plays a key role in mediating bacteria-host interaction and pathogen dissemination in the host. We show that GtrS and GltR form a two-component system that regulates the expression from the promoters Pedd/gap-1, PoprB and Pglk, which control the expression of genes involved in glucose metabolism and transport. In addition, the GtrS/GltR pair regulates the expression of toxA that encodes exotoxin A, the primary virulence factor. Microcalorimetry-based ligand screening of the recombinant GtrS ligand-binding domain revealed specific binding of 2-ketogluconate (2-KG) (KD=5 μM) and 6-phosphogluconate (KD=98 μM). These effectors accelerate GtrS autophosphorylation, with concomitant transphosphorylation of GltR leading to a three-fold increase in transcription. Surprisingly, in vivo a similar increase in expression from the above promoters was observed for the mutant deficient in GltR regardless of the presence of effectors. The GltR operator site was found to contain the consensus sequence 5'-tgGTTTTTc-3'. We propose that 2-KG is a key metabolite in the stringent transcriptional control of genes involved in virulence and glucose metabolism. We show that GltR is a transcriptional repressor that is released from DNA upon phosphorylation., (© The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.)
- Published
- 2014
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39. Interspecies signalling: Pseudomonas putida efflux pump TtgGHI is activated by indole to increase antibiotic resistance.
- Author
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Molina-Santiago C, Daddaoua A, Fillet S, Duque E, and Ramos JL
- Subjects
- Anti-Bacterial Agents metabolism, Anti-Bacterial Agents pharmacology, Bacterial Proteins genetics, Escherichia coli metabolism, Indoles metabolism, Membrane Transport Proteins genetics, Pseudomonas putida genetics, Pseudomonas putida metabolism, Signal Transduction, Transcription, Genetic drug effects, Bacterial Proteins metabolism, Drug Resistance, Bacterial genetics, Indoles pharmacology, Membrane Transport Proteins metabolism, Pseudomonas putida drug effects
- 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., (© 2013 Society for Applied Microbiology and John Wiley & Sons Ltd.)
- Published
- 2014
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40. Bactericidal and bacteriostatic antibiotics and the Fenton reaction.
- Author
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Molina-Santiago C and Ramos JL
- Subjects
- Oxidation-Reduction, Reactive Oxygen Species toxicity, Anti-Bacterial Agents metabolism, Escherichia coli drug effects, Escherichia coli metabolism, Hydrogen Peroxide metabolism, Iron metabolism, Pseudomonas aeruginosa drug effects, Pseudomonas aeruginosa metabolism
- Abstract
In gammaproteobacteria ROS are not exclusively responsible for the activity of bactericidal compounds. Future research is required to determine whether the high-valence FeO2+ formed in the presence of bactericidal compounds enhances killing in addition to the direct inhibition of cell-wall assembly, protein synthesis or interference with DNA metabolism., (© 2014 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.)
- Published
- 2014
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41. Identification of new residues involved in intramolecular signal transmission in a prokaryotic transcriptional repressor.
- Author
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Molina-Santiago C, Daddaoua A, Fillet S, Krell T, Morel B, Duque E, and Ramos JL
- Subjects
- Amino-Acid N-Acetyltransferase, Bacterial Proteins genetics, DNA, Bacterial, Models, Molecular, Mutagenesis, Site-Directed, Mutation, Protein Binding, Protein Conformation, Protein Stability, Pseudomonas putida genetics, Bacterial Proteins metabolism, Gene Expression Regulation, Bacterial physiology, Pseudomonas putida metabolism, Signal Transduction physiology, Transcription, Genetic physiology
- Abstract
TtgV is a member of the IclR family of transcriptional regulators. This regulator controls its own expression and that of the ttgGHI operon, which encodes an RND efflux pump. TtgV has two domains: a GAF-like domain harboring the effector-binding pocket and a helix-turn-helix (HTH) DNA-binding domain, which are linked by a long extended helix. When TtgV is bound to DNA, a kink at residue 86 in the extended helix gives rise to 2 helices. TtgV contacts DNA mainly through a canonical recognition helix, but its three-dimensional structure bound to DNA revealed that two residues, R19 and S35, outside the HTH motif, directly contact DNA. Effector binding to TtgV releases it from DNA; when this occurs, the kink at Q86 is lost and residues R19 and S35 are displaced due to the reorganization of the turn involving residues G44 and P46. Mutants of TtgV were generated at positions 19, 35, 44, 46, and 86 by site-directed mutagenesis to further analyze their role. Mutant proteins were purified to homogeneity, and differential scanning calorimetry (DSC) studies revealed that all mutants, except the Q86N mutant, unfold in a single event, suggesting conservation of the three-dimensional organization. All mutant variants bound effectors with an affinity similar to that of the parental protein. R19A, S35A, G44A, Q86N, and Q86E mutants did not bind DNA. The Q86A mutant was able to bind to DNA but was only partially released from its target operator in response to effectors. These results are discussed in the context of intramolecular signal transmission from the effector binding pocket to the DNA binding domain.
- Published
- 2014
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42. Fructooligosacharides reduce Pseudomonas aeruginosa PAO1 pathogenicity through distinct mechanisms.
- Author
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Ortega-González M, Sánchez de Medina F, Molina-Santiago C, López-Posadas R, Pacheco D, Krell T, Martínez-Augustin O, and Abdelali D
- Subjects
- ADP Ribose Transferases metabolism, Animals, Bacterial Proteins genetics, Bacterial Proteins metabolism, Bacterial Toxins metabolism, Biofilms growth & development, Blotting, Western, Cell Line, Cells, Cultured, DNA-Binding Proteins genetics, DNA-Binding Proteins metabolism, Epithelial Cells drug effects, Epithelial Cells metabolism, Epithelial Cells microbiology, Exotoxins metabolism, Female, Insulin pharmacology, Interleukin-10 metabolism, Interleukin-6 metabolism, Macrophages metabolism, Macrophages microbiology, Mutation, NF-kappa B metabolism, Pseudomonas aeruginosa genetics, Pseudomonas aeruginosa pathogenicity, Rats, Rats, Wistar, Signal Transduction drug effects, Transcription Factors genetics, Transcription Factors metabolism, Tumor Necrosis Factor-alpha metabolism, Virulence genetics, Virulence Factors metabolism, Pseudomonas aeruginosa Exotoxin A, Biofilms drug effects, Cytokines metabolism, Macrophages drug effects, Oligosaccharides pharmacology, Pseudomonas aeruginosa drug effects
- Abstract
Pseudomonas aeruginosa is ubiquitously present in the environment and acts as an opportunistic pathogen on humans, animals and plants. We report here the effects of the prebiotic polysaccharide inulin and its hydrolysed form FOS on this bacterium. FOS was found to inhibit bacterial growth of strain PAO1, while inulin did not affect growth rate or yield in a significant manner. Inulin stimulated biofilm formation, whereas a dramatic reduction of the biofilm formation was observed in the presence of FOS. Similar opposing effects were observed for bacterial motility, where FOS inhibited the swarming and twitching behaviour whereas inulin caused its stimulation. In co-cultures with eukaryotic cells (macrophages) FOS and, to a lesser extent, inulin reduced the secretion of the inflammatory cytokines IL-6, IL-10 and TNF-α. Western blot experiments indicated that the effects mediated by FOS in macrophages are associated with a decreased activation of the NF-κB pathway. Since FOS and inulin stimulate pathway activation in the absence of bacteria, the FOS mediated effect is likely to be of indirect nature, such as via a reduction of bacterial virulence. Further, this modulatory effect is observed also with the highly virulent ptxS mutated strain. Co-culture experiments of P. aeruginosa with IEC18 eukaryotic cells showed that FOS reduces the concentration of the major virulence factor, exotoxin A, suggesting that this is a possible mechanism for the reduction of pathogenicity. The potential of these compounds as components of antibacterial and anti-inflammatory cocktails is discussed.
- Published
- 2014
- Full Text
- View/download PDF
43. Antibiotic resistance determinants in a Pseudomonas putida strain isolated from a hospital.
- Author
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Molina L, Udaondo Z, Duque E, Fernández M, Molina-Santiago C, Roca A, Porcel M, de la Torre J, Segura A, Plesiat P, Jeannot K, and Ramos JL
- Subjects
- Amino Acid Sequence, Anti-Bacterial Agents pharmacology, Bacterial Proteins chemistry, Chromosomes, Bacterial genetics, Drug Resistance, Microbial drug effects, Genome, Bacterial genetics, Genomic Islands genetics, Humans, Microbial Sensitivity Tests, Molecular Sequence Data, Plasmids genetics, Pseudomonas putida drug effects, Sequence Analysis, DNA, Drug Resistance, Microbial genetics, Hospitals, Pseudomonas putida genetics, Pseudomonas putida isolation & purification
- Abstract
Environmental microbes harbor an enormous pool of antibiotic and biocide resistance genes that can impact the resistance profiles of animal and human pathogens via horizontal gene transfer. Pseudomonas putida strains are ubiquitous in soil and water but have been seldom isolated from humans. We have established a collection of P. putida strains isolated from in-patients in different hospitals in France. One of the isolated strains (HB3267) kills insects and is resistant to the majority of the antibiotics used in laboratories and hospitals, including aminoglycosides, ß-lactams, cationic peptides, chromoprotein enediyne antibiotics, dihydrofolate reductase inhibitors, fluoroquinolones and quinolones, glycopeptide antibiotics, macrolides, polyketides and sulfonamides. Similar to other P. putida clinical isolates the strain was sensitive to amikacin. To shed light on the broad pattern of antibiotic resistance, which is rarely found in clinical isolates of this species, the genome of this strain was sequenced and analysed. The study revealed that the determinants of multiple resistance are both chromosomally-borne as well as located on the pPC9 plasmid. Further analysis indicated that pPC9 has recruited antibiotic and biocide resistance genes from environmental microorganisms as well as from opportunistic and true human pathogens. The pPC9 plasmid is not self-transmissible, but can be mobilized by other bacterial plasmids making it capable of spreading antibiotic resistant determinants to new hosts.
- Published
- 2014
- Full Text
- View/download PDF
44. Antibiotic adjuvants: identification and clinical use.
- Author
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Bernal P, Molina-Santiago C, Daddaoua A, and Llamas MA
- Subjects
- Anti-Bacterial Agents pharmacology, Bacterial Infections drug therapy, Humans, Adjuvants, Pharmaceutic isolation & purification, Adjuvants, Pharmaceutic therapeutic use, Anti-Bacterial Agents therapeutic use, Bacterial Infections microbiology, Drug Resistance, Bacterial drug effects
- Published
- 2013
- Full Text
- View/download PDF
45. Evolution of antibiotic resistance, catabolic pathways and niche colonization.
- Author
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Molina-Santiago C, Udaondo Z, Marin A, García-Salamanca A, Michán C, Daniels C, Molina L, and Ramos JL
- Subjects
- Anti-Bacterial Agents isolation & purification, Bacteria genetics, Biodiversity, Biotechnology methods, Metagenome, Bacteria drug effects, Bacteria metabolism, Drug Resistance, Bacterial, Metabolic Networks and Pathways
- Published
- 2012
- Full Text
- View/download PDF
46. Mechanisms of resistance to chloramphenicol in Pseudomonas putida KT2440.
- Author
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Fernández M, Conde S, de la Torre J, Molina-Santiago C, Ramos JL, and Duque E
- Subjects
- Bacterial Proteins genetics, Culture Media, DNA Transposable Elements, Gene Expression Profiling, Microbial Sensitivity Tests, Mutation, Oligonucleotide Array Sequence Analysis, Pseudomonas putida genetics, Pseudomonas putida growth & development, Pseudomonas putida metabolism, Transcriptome, Anti-Bacterial Agents pharmacology, Bacterial Proteins metabolism, Chloramphenicol pharmacology, Drug Resistance, Bacterial, Gene Expression Regulation, Bacterial, Pseudomonas putida drug effects
- Abstract
Pseudomonas putida KT2440 is a chloramphenicol-resistant bacterium that is able to grow in the presence of this antibiotic at a concentration of up to 25 μg/ml. Transcriptomic analyses revealed that the expression profile of 102 genes changed in response to this concentration of chloramphenicol in the culture medium. The genes that showed altered expression include those involved in general metabolism, cellular stress response, gene regulation, efflux pump transporters, and protein biosynthesis. Analysis of a genome-wide collection of mutants showed that survival of a knockout mutant in the TtgABC resistance-nodulation-division (RND) efflux pump and mutants in the biosynthesis of pyrroloquinoline (PQQ) were compromised in the presence of chloramphenicol. The analysis also revealed that an ABC extrusion system (PP2669/PP2668/PP2667) and the AgmR regulator (PP2665) were needed for full resistance toward chloramphenicol. Transcriptional arrays revealed that AgmR controls the expression of the pqq genes and the operon encoding the ABC extrusion pump from the promoter upstream of open reading frame (ORF) PP2669.
- Published
- 2012
- Full Text
- View/download PDF
47. Directed evolution, natural products for cancer chemotherapy, and micro-biosensing robots.
- Author
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Daniels C, Ramos JL, Molina-Santiago C, and Michán C
- Subjects
- Animals, Antineoplastic Agents therapeutic use, Bacteria chemistry, Bacteria metabolism, Biological Products therapeutic use, Biosensing Techniques methods, Directed Molecular Evolution, Fungi chemistry, Fungi metabolism, Humans, Antineoplastic Agents metabolism, Bacteria genetics, Biological Products metabolism, Biosensing Techniques instrumentation, Fungi genetics, Neoplasms drug therapy
- Published
- 2011
- Full Text
- View/download PDF
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