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Batianis C, van Rosmalen RP, Major M, van Ee C, Kasiotakis A, Weusthuis RA, Martins Dos Santos VAP. A tunable metabolic valve for precise growth control and increased product formation in Pseudomonas putida. Metab Eng 2023; 75:47-57. [PMID: 36244546 DOI: 10.1016/j.ymben.2022.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 10/06/2022] [Accepted: 10/08/2022] [Indexed: 11/06/2022]
Abstract
Metabolic engineering of microorganisms aims to design strains capable of producing valuable compounds under relevant industrial conditions and in an economically competitive manner. From this perspective, and beyond the need for a catalyst, biomass is essentially a cost-intensive, abundant by-product of a microbial conversion. Yet, few broadly applicable strategies focus on the optimal balance between product and biomass formation. Here, we present a genetic control module that can be used to precisely modulate growth of the industrial bacterial chassis Pseudomonas putida KT2440. The strategy is based on the controllable expression of the key metabolic enzyme complex pyruvate dehydrogenase (PDH) which functions as a metabolic valve. By tuning the PDH activity, we accurately controlled biomass formation, resulting in six distinct growth rates with parallel overproduction of excess pyruvate. We deployed this strategy to identify optimal growth patterns that improved the production yield of 2-ketoisovalerate and lycopene by 2.5- and 1.38-fold, respectively. This ability to dynamically steer fluxes to balance growth and production substantially enhances the potential of this remarkable microbial chassis for a wide range of industrial applications.
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Affiliation(s)
- Christos Batianis
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, the Netherlands
| | - Rik P van Rosmalen
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, the Netherlands
| | - Monika Major
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, the Netherlands
| | - Cheyenne van Ee
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, the Netherlands
| | - Alexandros Kasiotakis
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, the Netherlands
| | - Ruud A Weusthuis
- Bioprocess Engineering, Wageningen University and Research, Wageningen, the Netherlands
| | - Vitor A P Martins Dos Santos
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, the Netherlands; Bioprocess Engineering, Wageningen University and Research, Wageningen, the Netherlands; LifeGlimmer GmbH, Berlin, Germany.
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2
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Delangiz N, Aliyar S, Pashapoor N, Nobaharan K, Asgari Lajayer B, Rodríguez-Couto S. Can polymer-degrading microorganisms solve the bottleneck of plastics' environmental challenges? CHEMOSPHERE 2022; 294:133709. [PMID: 35074325 DOI: 10.1016/j.chemosphere.2022.133709] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 11/27/2021] [Accepted: 01/18/2022] [Indexed: 06/14/2023]
Abstract
Increasing world population and industrial activities have enhanced anthropogenic pollution, plastic pollution being especially alarming. So, plastics should be recycled and/or make them biodegradable. Chemical and physical remediating methods are usually energy consuming and costly. In addition, they are not ecofriendly and usually produce toxic byproducts. Bioremediation is a proper option as it is cost-efficient and environmentally friendly. Plastic production and consumption are increasing daily, and, as a consequence, more microorganisms are exposed to these nonbiodegradable polymers. Therefore, investigating new efficient microorganisms and increasing the knowledge about their biology can pave the way for efficient and feasible plastic bioremediation processes. In this sense, omics, systems biology and bioinformatics are three important fields to analyze the biodegradation pathways in microorganisms. Based on the above-mentioned technologies, researchers can engineer microorganisms with specific desired properties to make bioremediation more efficient.
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Affiliation(s)
- Nasser Delangiz
- Department of Plant Biotechnology and Breeding, Faculty of Agriculture, University of Tabriz, Tabriz, Iran.
| | - Sajad Aliyar
- Department of Soil Science, Faculty of Agriculture, University of Tabriz, Tabriz, Iran
| | - Neda Pashapoor
- Department of Soil Science, Faculty of Agriculture, Urmia University, Urmia, Iran
| | | | - Behnam Asgari Lajayer
- Department of Soil Science, Faculty of Agriculture, University of Tabriz, Tabriz, Iran.
| | - Susana Rodríguez-Couto
- Department of Separation Science, LUT School of Engineering Science, LUT University, Sammonkatu 12, FI-50130 Mikkeli, Finland
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3
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Current research on simultaneous oxidation of aliphatic and aromatic hydrocarbons by bacteria of genus Pseudomonas. Folia Microbiol (Praha) 2022; 67:591-604. [PMID: 35318574 DOI: 10.1007/s12223-022-00966-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 03/15/2022] [Indexed: 11/04/2022]
Abstract
One of the most frequently used methods for elimination of oil pollution is the use of biological preparations based on oil-degrading microorganisms. Such microorganisms often relate to bacteria of the genus Pseudomonas. Pseudomonads are ubiquitous microorganisms that often have the ability to oxidize various pollutants, including oil hydrocarbons. To date, individual biochemical pathways of hydrocarbon degradation and the organization of the corresponding genes have been studied in detail. Almost all studies of this kind have been performed on degraders of individual hydrocarbons belonging to a single particular class. Microorganisms capable of simultaneous degradation of aliphatic and aromatic hydrocarbons are very poorly studied. Most of the works on such objects have been devoted only to phenotype characteristic and some to genetic studies. To identify the patterns of interaction of several metabolic systems depending on the growth conditions, the most promising are such approaches as transcriptomics and proteomics, which make it possible to obtain a comprehensive assessment of changes in the expression of hundreds of genes and proteins at the same time. This review summarizes the existing data on bacteria of the genus Pseudomonas capable of the simultaneous oxidation of hydrocarbons of different classes (alkanes, monoaromatics, and polyaromatics) and presents the most important results obtained in the studies on the biodegradation of hydrocarbons by representatives of this genus using methods of transcriptomic and proteomic analyses.
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Wirth NT, Nikel PI. Combinatorial pathway balancing provides biosynthetic access to 2-fluoro- cis, cis-muconate in engineered Pseudomonas putida. CHEM CATALYSIS 2021; 1:1234-1259. [PMID: 34977847 PMCID: PMC8711041 DOI: 10.1016/j.checat.2021.09.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 08/15/2021] [Accepted: 08/31/2021] [Indexed: 12/18/2022]
Abstract
The wealth of bio-based building blocks produced by engineered microorganisms seldom include halogen atoms. Muconate is a platform chemical with a number of industrial applications that could be broadened by introducing fluorine atoms to tune its physicochemical properties. The soil bacterium Pseudomonas putida naturally assimilates benzoate via the ortho-cleavage pathway with cis,cis-muconate as intermediate. Here, we harnessed the native enzymatic machinery (encoded within the ben and cat gene clusters) to provide catalytic access to 2-fluoro-cis,cis-muconate (2-FMA) from fluorinated benzoates. The reactions in this pathway are highly imbalanced, leading to accumulation of toxic intermediates and limited substrate conversion. By disentangling regulatory patterns of ben and cat in response to fluorinated effectors, metabolic activities were adjusted to favor 2-FMA biosynthesis. After implementing this combinatorial approach, engineered P. putida converted 3-fluorobenzoate to 2-FMA at the maximum theoretical yield. Hence, this study illustrates how synthetic biology can expand the diversity of nature's biochemical catalysis.
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Affiliation(s)
- Nicolas T Wirth
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
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Cook TB, Jacobson TB, Venkataraman MV, Hofstetter H, Amador-Noguez D, Thomas MG, Pfleger BF. Stepwise genetic engineering of Pseudomonas putida enables robust heterologous production of prodigiosin and glidobactin A. Metab Eng 2021; 67:112-124. [PMID: 34175462 DOI: 10.1016/j.ymben.2021.06.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 06/14/2021] [Accepted: 06/19/2021] [Indexed: 12/21/2022]
Abstract
Polyketide synthases (PKS) and nonribosomal peptide synthetases (NRPS) comprise biosynthetic pathways that provide access to diverse, often bioactive natural products. Metabolic engineering can improve production metrics to support characterization and drug-development studies, but often native hosts are difficult to genetically manipulate and/or culture. For this reason, heterologous expression is a common strategy for natural product discovery and characterization. Many bacteria have been developed to express heterologous biosynthetic gene clusters (BGCs) for producing polyketides and nonribosomal peptides. In this article, we describe tools for using Pseudomonas putida, a Gram-negative soil bacterium, as a heterologous host for producing natural products. Pseudomonads are known to produce many natural products, but P. putida production titers have been inconsistent in the literature and often low compared to other hosts. In recent years, synthetic biology tools for engineering P. putida have greatly improved, but their application towards production of natural products is limited. To demonstrate the potential of P. putida as a heterologous host, we introduced BGCs encoding the synthesis of prodigiosin and glidobactin A, two bioactive natural products synthesized from a combination of PKS and NRPS enzymology. Engineered strains exhibited robust production of both compounds after a single chromosomal integration of the corresponding BGC. Next, we took advantage of a set of genome-editing tools to increase titers by modifying transcription and translation of the BGCs and increasing the availability of auxiliary proteins required for PKS and NRPS activity. Lastly, we discovered genetic modifications to P. putida that affect natural product synthesis, including a strategy for removing a carbon sink that improves product titers. These efforts resulted in production strains capable of producing 1.1 g/L prodigiosin and 470 mg/L glidobactin A.
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Affiliation(s)
- Taylor B Cook
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Tyler B Jacobson
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Maya V Venkataraman
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Heike Hofstetter
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Daniel Amador-Noguez
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA; Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, USA
| | - Michael G Thomas
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA; Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, USA
| | - Brian F Pfleger
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA; Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, USA.
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Durante-Rodríguez G, Páez-Espino D, de Lorenzo V. A Bifan Motif Shaped by ArsR1, ArsR2, and Their Cognate Promoters Frames Arsenic Tolerance of Pseudomonas putida. Front Microbiol 2021; 12:641440. [PMID: 33776973 PMCID: PMC7994332 DOI: 10.3389/fmicb.2021.641440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 02/12/2021] [Indexed: 11/13/2022] Open
Abstract
Prokaryotic tolerance to inorganic arsenic is a widespread trait habitually determined by operons encoding an As (III)-responsive repressor (ArsR), an As (V)-reductase (ArsC), and an As (III)-export pump (ArsB), often accompanied by other complementary genes. Enigmatically, the genomes of many environmental bacteria typically contain two or more copies of this basic genetic device arsRBC. To shed some light on the logic of such apparently unnecessary duplication(s) we have inspected the regulation—together and by separate—of the two ars clusters borne by the soil bacterium Pseudomonas putida strain KT2440, in particular the cross talk between the two repressors ArsR1/ArsR2 and the respective promoters. DNase I footprinting and gel retardation analyses of Pars1 and Pars2 with their matching regulators revealed non-identical binding sequences and interaction patterns for each of the systems. However, in vitro transcription experiments exposed that the repressors could downregulate each other’s promoters, albeit within a different set of parameters. The regulatory frame that emerges from these data corresponds to a particular type of bifan motif where all key interactions have a negative sign. The distinct regulatory architecture that stems from coexistence of various ArsR variants in the same cells could enter an adaptive advantage that favors the maintenance of the two proteins as separate repressors.
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Affiliation(s)
| | - David Páez-Espino
- Systems Biology Department, Centro Nacional de Biotecnología-CSIC, Madrid, Spain
| | - Víctor de Lorenzo
- Systems Biology Department, Centro Nacional de Biotecnología-CSIC, Madrid, Spain
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Cofactor Specificity of Glucose-6-Phosphate Dehydrogenase Isozymes in Pseudomonas putida Reveals a General Principle Underlying Glycolytic Strategies in Bacteria. mSystems 2021; 6:6/2/e00014-21. [PMID: 33727391 PMCID: PMC8546961 DOI: 10.1128/msystems.00014-21] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Glucose-6-phosphate dehydrogenase (G6PDH) is widely distributed in nature and catalyzes the first committing step in the oxidative branch of the pentose phosphate (PP) pathway, feeding either the reductive PP or the Entner-Doudoroff pathway. Besides its role in central carbon metabolism, this dehydrogenase provides reduced cofactors, thereby affecting redox balance. Although G6PDH is typically considered to display specificity toward NADP+, some variants accept NAD+ similarly or even preferentially. Furthermore, the number of G6PDH isozymes encoded in bacterial genomes varies from none to more than four orthologues. On this background, we systematically analyzed the interplay of the three G6PDH isoforms of the soil bacterium Pseudomonas putida KT2440 from genomic, genetic, and biochemical perspectives. P. putida represents an ideal model to tackle this endeavor, as its genome harbors gene orthologues for most dehydrogenases in central carbon metabolism. We show that the three G6PDHs of strain KT2440 have different cofactor specificities and that the isoforms encoded by zwfA and zwfB carry most of the activity, acting as metabolic “gatekeepers” for carbon sources that enter at different nodes of the biochemical network. Moreover, we demonstrate how multiplication of G6PDH isoforms is a widespread strategy in bacteria, correlating with the presence of an incomplete Embden-Meyerhof-Parnas pathway. The abundance of G6PDH isoforms in these species goes hand in hand with low NADP+ affinity, at least in one isozyme. We propose that gene duplication and relaxation in cofactor specificity is an evolutionary strategy toward balancing the relative production of NADPH and NADH. IMPORTANCE Protein families have likely arisen during evolution by gene duplication and divergence followed by neofunctionalization. While this phenomenon is well documented for catabolic activities (typical of environmental bacteria that colonize highly polluted niches), the coexistence of multiple isozymes in central carbon catabolism remains relatively unexplored. We have adopted the metabolically versatile soil bacterium Pseudomonas putida KT2440 as a model to interrogate the physiological and evolutionary significance of coexisting glucose-6-phosphate dehydrogenase (G6PDH) isozymes. Our results show that each of the three G6PDHs in this bacterium display distinct biochemical properties, especially at the level of cofactor preference, impacting bacterial physiology in a carbon source-dependent fashion. Furthermore, the presence of multiple G6PDHs differing in NAD+ or NADP+ specificity in bacterial species strongly correlates with their predominant metabolic lifestyle. Our findings support the notion that multiplication of genes encoding cofactor-dependent dehydrogenases is a general evolutionary strategy toward achieving redox balance according to the growth conditions.
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8
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Whon TW, Shin NR, Kim JY, Roh SW. Omics in gut microbiome analysis. J Microbiol 2021; 59:292-297. [DOI: 10.1007/s12275-021-1004-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 02/09/2021] [Accepted: 02/10/2021] [Indexed: 12/13/2022]
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9
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Arce-Rodríguez A, Nikel PI, Calles B, Chavarría M, Platero R, Krell T, de Lorenzo V. Low CyaA expression and anti-cooperative binding of cAMP to CRP frames the scope of the cognate regulon of Pseudomonas putida. Environ Microbiol 2021; 23:1732-1749. [PMID: 33559269 DOI: 10.1111/1462-2920.15422] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 01/09/2021] [Accepted: 02/02/2021] [Indexed: 12/29/2022]
Abstract
Although the soil bacterium Pseudomonas putida KT2440 bears a bona fide adenylate cyclase gene (cyaA), intracellular concentrations of 3',5'-cyclic adenosine monophosphate (cAMP) are barely detectable. By using reporter technology and direct quantification of cAMP under various conditions, we show that such low levels of the molecule stem from the stringent regulation of its synthesis, efflux and degradation. Poor production of cAMP was the result of inefficient translation of cyaA mRNA. Moreover, deletion of the cAMP-phosphodiesterase pde gene led to intracellular accumulation of the cyclic nucleotide, exposing an additional cause of cAMP drain in vivo. But even such low levels of the signal sustained activation of promoters dependent on the cAMP-receptor protein (CRP). Genetic and biochemical evidence indicated that the phenomenon ultimately rose from the unusual binding parameters of cAMP to CRP. This included an ultratight cAMP-CrpP. putida affinity (KD of 45.0 ± 3.4 nM) and an atypical 1:1 effector/dimer stoichiometry that obeyed an infrequent anti-cooperative binding mechanism. It thus seems that keeping the same regulatory parts and their relational logic but changing the interaction parameters enables genetic devices to take over entirely different domains of the functional landscape.
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Affiliation(s)
- Alejandro Arce-Rodríguez
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, 38124, Germany
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, 2800, Denmark
| | - Belén Calles
- Systems Biology Department, Centro Nacional de Biotecnología-CSIC, Campus de Cantoblanco, Madrid, 28049, Spain
| | - Max Chavarría
- Escuela de Química and CIPRONA, Universidad de Costa Rica, San José, 2060, Costa Rica
| | - Raúl Platero
- Departamento de Bioquímica y Genómica Microbianas, Instituto de Investigaciones Biológicas Clemente Estable, MEC, Montevideo, Uruguay
| | - Tino Krell
- Department of Environmental Protection, Estación Experimental del Zaidín CSIC, Granada, 18008, Spain
| | - Victor de Lorenzo
- Systems Biology Department, Centro Nacional de Biotecnología-CSIC, Campus de Cantoblanco, Madrid, 28049, Spain
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Dabrowska D, Mozejko-Ciesielska J, Pokój T, Ciesielski S. Transcriptome Changes in Pseudomonas putida KT2440 during Medium-Chain-Length Polyhydroxyalkanoate Synthesis Induced by Nitrogen Limitation. Int J Mol Sci 2020; 22:ijms22010152. [PMID: 33375721 PMCID: PMC7801951 DOI: 10.3390/ijms22010152] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 12/16/2020] [Accepted: 12/21/2020] [Indexed: 11/16/2022] Open
Abstract
Pseudomonas putida’s versatility and metabolic flexibility make it an ideal biotechnological platform for producing valuable chemicals, such as medium-chain-length polyhydroxyalkanoates (mcl-PHAs), which are considered the next generation bioplastics. This bacterium responds to environmental stimuli by rearranging its metabolism to improve its fitness and increase its chances of survival in harsh environments. Mcl-PHAs play an important role in central metabolism, serving as a reservoir of carbon and energy. Due to the complexity of mcl-PHAs’ metabolism, the manner in which P. putida changes its transcriptome to favor mcl-PHA synthesis in response to environmental stimuli remains unclear. Therefore, our objective was to investigate how the P. putida KT2440 wild type and mutants adjust their transcriptomes to synthesize mcl-PHAs in response to nitrogen limitation when supplied with sodium gluconate as an external carbon source. We found that, under nitrogen limitation, mcl-PHA accumulation is significantly lower in the mutant deficient in the stringent response than in the wild type or the rpoN mutant. Transcriptome analysis revealed that, under N-limiting conditions, 24 genes were downregulated and 21 were upregulated that were common to all three strains. Additionally, potential regulators of these genes were identified: the global anaerobic regulator (Anr, consisting of FnrA, Fnrb, and FnrC), NorR, NasT, the sigma54-dependent transcriptional regulator, and the dual component NtrB/NtrC regulator all appear to play important roles in transcriptome rearrangement under N-limiting conditions. The role of these regulators in mcl-PHA synthesis is discussed.
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Affiliation(s)
- Dorota Dabrowska
- Department of Environmental Biotechnology, University of Warmia and Mazury in Olsztyn, 10-719 Olsztyn, Poland; (D.D.); (T.P.)
| | - Justyna Mozejko-Ciesielska
- Department of Microbiology and Mycology, University of Warmia and Mazury in Olsztyn, 10-719 Olsztyn, Poland;
| | - Tomasz Pokój
- Department of Environmental Biotechnology, University of Warmia and Mazury in Olsztyn, 10-719 Olsztyn, Poland; (D.D.); (T.P.)
| | - Slawomir Ciesielski
- Department of Environmental Biotechnology, University of Warmia and Mazury in Olsztyn, 10-719 Olsztyn, Poland; (D.D.); (T.P.)
- Correspondence: ; Tel.: +48-89-5234162
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11
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Weimer A, Kohlstedt M, Volke DC, Nikel PI, Wittmann C. Industrial biotechnology of Pseudomonas putida: advances and prospects. Appl Microbiol Biotechnol 2020; 104:7745-7766. [PMID: 32789744 PMCID: PMC7447670 DOI: 10.1007/s00253-020-10811-9] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 07/23/2020] [Accepted: 08/02/2020] [Indexed: 11/17/2022]
Abstract
Pseudomonas putida is a Gram-negative, rod-shaped bacterium that can be encountered in diverse ecological habitats. This ubiquity is traced to its remarkably versatile metabolism, adapted to withstand physicochemical stress, and the capacity to thrive in harsh environments. Owing to these characteristics, there is a growing interest in this microbe for industrial use, and the corresponding research has made rapid progress in recent years. Hereby, strong drivers are the exploitation of cheap renewable feedstocks and waste streams to produce value-added chemicals and the steady progress in genetic strain engineering and systems biology understanding of this bacterium. Here, we summarize the recent advances and prospects in genetic engineering, systems and synthetic biology, and applications of P. putida as a cell factory. KEY POINTS: • Pseudomonas putida advances to a global industrial cell factory. • Novel tools enable system-wide understanding and streamlined genomic engineering. • Applications of P. putida range from bioeconomy chemicals to biosynthetic drugs.
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Affiliation(s)
- Anna Weimer
- Institute of Systems Biotechnology, Saarland University, Campus A1.5, 66123, Saarbrücken, Germany
| | - Michael Kohlstedt
- Institute of Systems Biotechnology, Saarland University, Campus A1.5, 66123, Saarbrücken, Germany
| | - Daniel C Volke
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Christoph Wittmann
- Institute of Systems Biotechnology, Saarland University, Campus A1.5, 66123, Saarbrücken, Germany.
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12
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Collins AJ, Smith TJ, Sondermann H, O'Toole GA. From Input to Output: The Lap/c-di-GMP Biofilm Regulatory Circuit. Annu Rev Microbiol 2020; 74:607-631. [PMID: 32689917 DOI: 10.1146/annurev-micro-011520-094214] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Biofilms are the dominant bacterial lifestyle. The regulation of the formation and dispersal of bacterial biofilms has been the subject of study in many organisms. Over the last two decades, the mechanisms of Pseudomonas fluorescens biofilm formation and regulation have emerged as among the best understood of any bacterial biofilm system. Biofilm formation by P. fluorescens occurs through the localization of an adhesin, LapA, to the outer membrane via a variant of the classical type I secretion system. The decision between biofilm formation and dispersal is mediated by LapD, a c-di-GMP receptor, and LapG, a periplasmic protease, which together control whether LapA is retained or released from the cell surface. LapA localization is also controlled by a complex network of c-di-GMP-metabolizing enzymes. This review describes the current understanding of LapA-mediated biofilm formation by P. fluorescens and discusses several emerging models for the regulation and function of this adhesin.
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Affiliation(s)
- Alan J Collins
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.,Geisel School of Medicine at Dartmouth, Hanover, New Hampshire 03755, USA;
| | - T Jarrod Smith
- Geisel School of Medicine at Dartmouth, Hanover, New Hampshire 03755, USA; .,Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, USA
| | | | - George A O'Toole
- Geisel School of Medicine at Dartmouth, Hanover, New Hampshire 03755, USA;
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13
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Volke DC, Friis L, Wirth NT, Turlin J, Nikel PI. Synthetic control of plasmid replication enables target- and self-curing of vectors and expedites genome engineering of Pseudomonas putida. Metab Eng Commun 2020; 10:e00126. [PMID: 32215253 PMCID: PMC7090339 DOI: 10.1016/j.mec.2020.e00126] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 02/23/2020] [Accepted: 02/29/2020] [Indexed: 02/07/2023] Open
Abstract
Genome engineering of non-conventional microorganisms calls for the development of dedicated synthetic biology tools. Pseudomonas putida is a Gram-negative, non-pathogenic soil bacterium widely used for metabolic engineering owing to its versatile metabolism and high levels of tolerance to different types of stress. Genome editing of P. putida largely relies on homologous recombination events, assisted by helper plasmid-based expression of genes encoding DNA modifying enzymes. Plasmid curing from selected isolates is the most tedious and time-consuming step of this procedure, and implementing commonly used methods to this end in P. putida (e.g. temperature-sensitive replicons) is often impractical. To tackle this issue, we have developed a toolbox for both target- and self-curing of plasmid DNA in Pseudomonas species. Our method enables plasmid-curing in a simple cultivation step by combining in vivo digestion of vectors by the I-SceI homing nuclease with synthetic control of plasmid replication, triggered by the addition of a cheap chemical inducer (3-methylbenzoate) to the medium. The system displays an efficiency of vector curing >90% and the screening of plasmid-free clones is greatly facilitated by the use of fluorescent markers that can be selected according to the application intended. Furthermore, quick genome engineering of P. putida using self-curing plasmids is demonstrated through genome reduction of the platform strain EM42 by eliminating all genes encoding β-lactamases, the catabolic ben gene cluster, and the pyoverdine synthesis machinery. Physiological characterization of the resulting streamlined strain, P. putida SEM10, revealed advantageous features that could be exploited for metabolic engineering. Plasmid-curing is the most time-consuming step in genome engineering approaches. We have developed a system for easy target- and self-curing of plasmid DNA. Synthetic control of replication and highly-specific in vivo DNA digestion were used. Plasmid curing with this system displays an efficiency >90% in a 24-h cultivation. Quick genome engineering facilitated genome reduction of P. putida.
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Affiliation(s)
- Daniel C Volke
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs Lyngby, Denmark
| | - Laura Friis
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs Lyngby, Denmark
| | - Nicolas T Wirth
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs Lyngby, Denmark
| | - Justine Turlin
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs Lyngby, Denmark
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs Lyngby, Denmark
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14
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Contextual Flexibility in Pseudomonas aeruginosa Central Carbon Metabolism during Growth in Single Carbon Sources. mBio 2020; 11:mBio.02684-19. [PMID: 32184246 PMCID: PMC7078475 DOI: 10.1128/mbio.02684-19] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Pseudomonas aeruginosa is an opportunistic human pathogen that is well known for causing infections in the airways of people with cystic fibrosis. Although it is clear that P. aeruginosa is metabolically well adapted to life in the CF lung, little is currently known about how the organism metabolizes the nutrients available in the airways. In this work, we used a combination of gene expression and isotope tracer (“fluxomic”) analyses to find out exactly where the input carbon goes during growth on two CF-relevant carbon sources, acetate and glycerol (derived from the breakdown of lung surfactant). We found that carbon is routed (“fluxed”) through very different pathways during growth on these substrates and that this is accompanied by an unexpected remodeling of the cell’s electron transfer pathways. Having access to this “blueprint” is important because the metabolism of P. aeruginosa is increasingly being recognized as a target for the development of much-needed antimicrobial agents. Pseudomonas aeruginosa is an opportunistic human pathogen, particularly noted for causing infections in the lungs of people with cystic fibrosis (CF). Previous studies have shown that the gene expression profile of P. aeruginosa appears to converge toward a common metabolic program as the organism adapts to the CF airway environment. However, we still have only a limited understanding of how these transcriptional changes impact metabolic flux at the systems level. To address this, we analyzed the transcriptome, proteome, and fluxome of P. aeruginosa grown on glycerol or acetate. These carbon sources were chosen because they are the primary breakdown products of an airway surfactant, phosphatidylcholine, which is known to be a major carbon source for P. aeruginosa in CF airways. We show that the fluxes of carbon throughout central metabolism are radically different among carbon sources. For example, the newly recognized “EDEMP cycle” (which incorporates elements of the Entner-Doudoroff [ED] pathway, the Embden-Meyerhof-Parnas [EMP] pathway, and the pentose phosphate [PP] pathway) plays an important role in supplying NADPH during growth on glycerol. In contrast, the EDEMP cycle is attenuated during growth on acetate, and instead, NADPH is primarily supplied by the reaction catalyzed by isocitrate dehydrogenase(s). Perhaps more importantly, our proteomic and transcriptomic analyses revealed a global remodeling of gene expression during growth on the different carbon sources, with unanticipated impacts on aerobic denitrification, electron transport chain architecture, and the redox economy of the cell. Collectively, these data highlight the remarkable metabolic plasticity of P. aeruginosa; that plasticity allows the organism to seamlessly segue between different carbon sources, maximizing the energetic yield from each.
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15
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Wang F, Wan Y, Yin K, Wei Y, Wang B, Yu X, Ni Y, Zheng J, Huang T, Song M, Li D. Lower Circulating Branched-Chain Amino Acid Concentrations Among Vegetarians are Associated with Changes in Gut Microbial Composition and Function. Mol Nutr Food Res 2019; 63:e1900612. [PMID: 31703241 DOI: 10.1002/mnfr.201900612] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 09/29/2019] [Indexed: 12/20/2022]
Abstract
SCOPE Vegetarian diets confer health benefits to many cardiometabolic diseases, although whether and how gut microbiota in vegetarians contributes to host metabolism remains unclear. Thus, the aim is to explore the possible links between the gut microbiota and circulating gut microbiota-host co-metabolites among vegetarians and omnivores. METHODS AND RESULTS Fecal and serum samples from 36 adults following a vegan, lacto-ovo vegetarian, or omnivorous diet are collected. A 16S rRNA gene, metagenome, metatranscriptome, and metabolome integrated multi-omics approach is adopted to profile fecal microbial composition and functionality and circulating gut microbiota-host co-metabolites. 16S rRNA gene and metagenomic sequencing suggest a significant difference in gut microbial composition between the two vegetarian groups and the omnivorous group at the family, genus, and species level. Metabolomic analysis reveals that circulating branched-chain amino acids (BCAAs)-valine, leucine, and isoleucine-are significantly lower in the two vegetarian groups than those in the omnivorous group. In line with the lower concentrations of BCAAs, metatranscriptomic analysis shows that the gut microbial pathway for the degradation of BCAAs is significantly upregulated among vegetarians compared with the omnivores. CONCLUSIONS The results indicate that gut microbiota plays an important role in the modulation of circulating BCAAs among vegetarians.
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Affiliation(s)
- Fenglei Wang
- Institute of Nutrition & Health, Qingdao University, Qingdao, 266071, China.,Department of Food Science and Nutrition, Zhejiang University, Hangzhou, 310058, China.,Department of Nutrition, Harvard T. H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Yi Wan
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou, 310058, China.,Department of Nutrition, Harvard T. H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Kanhua Yin
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Yaguang Wei
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Beibei Wang
- State Key Laboratory of Rice Biology & Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Xiaomei Yu
- Department of Clinical Laboratory, Zhejiang Hospital, Hangzhou, 310007, China
| | - Yan Ni
- The Children's Hospital, School of Medicine, Zhejiang University, Hangzhou, 310052, China
| | - Jusheng Zheng
- Institute of Basic Medical Science, Westlake Institute for Advanced Study, Westlake University, Hangzhou, 310024, China
| | - Tao Huang
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science Center, Beijing, 100191, China
| | - Mingyang Song
- Department of Nutrition, Harvard T. H. Chan School of Public Health, Boston, MA, 02115, USA.,Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA.,Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02108, USA.,Division of Gastroenterology, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Duo Li
- Institute of Nutrition & Health, Qingdao University, Qingdao, 266071, China.,Department of Food Science and Nutrition, Zhejiang University, Hangzhou, 310058, China
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16
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The effects of plant-based diets on the body and the brain: a systematic review. Transl Psychiatry 2019; 9:226. [PMID: 31515473 PMCID: PMC6742661 DOI: 10.1038/s41398-019-0552-0] [Citation(s) in RCA: 151] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 06/22/2019] [Accepted: 07/17/2019] [Indexed: 12/15/2022] Open
Abstract
Western societies notice an increasing interest in plant-based eating patterns such as vegetarian and vegan, yet potential effects on the body and brain are a matter of debate. Therefore, we systematically reviewed existing human interventional studies on putative effects of a plant-based diet on the metabolism and cognition, and what is known about the underlying mechanisms. Using the search terms "plant-based OR vegan OR vegetarian AND diet AND intervention" in PubMed filtered for clinical trials in humans retrieved 205 studies out of which 27, plus an additional search extending the selection to another five studies, were eligible for inclusion based on three independent ratings. We found robust evidence for short- to moderate-term beneficial effects of plant-based diets versus conventional diets (duration ≤ 24 months) on weight status, energy metabolism and systemic inflammation in healthy participants, obese and type-2 diabetes patients. Initial experimental studies proposed novel microbiome-related pathways, by which plant-based diets modulate the gut microbiome towards a favorable diversity of bacteria species, yet a functional "bottom up" signaling of plant-based diet-induced microbial changes remains highly speculative. In addition, little is known, based on interventional studies about cognitive effects linked to plant-based diets. Thus, a causal impact of plant-based diets on cognitive functions, mental and neurological health and respective underlying mechanisms has yet to be demonstrated. In sum, the increasing interest for plant-based diets raises the opportunity for developing novel preventive and therapeutic strategies against obesity, eating disorders and related comorbidities. Still, putative effects of plant-based diets on brain health and cognitive functions as well as the underlying mechanisms remain largely unexplored and new studies need to address these questions.
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17
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Adipositas, metabolische Komorbiditäten und Mikrobiommodulation in der Pädiatrie. Monatsschr Kinderheilkd 2019. [DOI: 10.1007/s00112-019-0689-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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18
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Hueso-Gil Á, Calles B, O'Toole GA, de Lorenzo V. Gross transcriptomic analysis of Pseudomonas putida for diagnosing environmental shifts. Microb Biotechnol 2019; 13:263-273. [PMID: 30957409 PMCID: PMC6922523 DOI: 10.1111/1751-7915.13404] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 03/10/2019] [Accepted: 03/12/2019] [Indexed: 01/24/2023] Open
Abstract
The biological regime of Pseudomonas putida (and any other bacterium) under given environmental conditions results from the hierarchical expression of sets of genes that become turned on and off in response to one or more physicochemical signals. In some cases, such signals are clearly defined, but in many others, cells are exposed to a whole variety of ill-defined inputs that occur simultaneously. Transcriptomic analyses of bacteria passed from a reference condition to a complex niche can thus expose both the type of signals that they experience during the transition and the functions involved in adaptation to the new scenario. In this article, we describe a complete protocol for generation of transcriptomes aimed at monitoring the physiological shift of P. putida between two divergent settings using as a simple case study the change between homogeneous, planktonic lifestyle in a liquid medium and growth on the surface of an agar plate. To this end, RNA was collected from P. putidaKT2440 cells at various times after growth in either condition, and the genome-wide transcriptional outputs were analysed. While the role of individual genes needs to be verified on a case-by-case basis, a gross inspection of the resulting profiles suggested cells that are cultured on solid media consistently had a higher translational and metabolic activity, stopped production of flagella and were conspicuously exposed to a strong oxidative stress. The herein described methodology is generally applicable to other circumstances for diagnosing lifestyle determinants of interest.
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Affiliation(s)
- Ángeles Hueso-Gil
- Systems Biology Program, Centro Nacional de Biotecnología-CSIC, Campus de Cantoblanco, Madrid, 28049, Spain
| | - Belén Calles
- Systems Biology Program, Centro Nacional de Biotecnología-CSIC, Campus de Cantoblanco, Madrid, 28049, Spain
| | - George A O'Toole
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, 03755, USA
| | - Víctor de Lorenzo
- Systems Biology Program, Centro Nacional de Biotecnología-CSIC, Campus de Cantoblanco, Madrid, 28049, Spain
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19
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D'Arrigo I, Cardoso JGR, Rennig M, Sonnenschein N, Herrgård MJ, Long KS. Analysis of Pseudomonas putida growth on non-trivial carbon sources using transcriptomics and genome-scale modelling. ENVIRONMENTAL MICROBIOLOGY REPORTS 2019; 11:87-97. [PMID: 30298597 DOI: 10.1111/1758-2229.12704] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 10/02/2018] [Accepted: 10/03/2018] [Indexed: 06/08/2023]
Abstract
Pseudomonas putida is characterized by a versatile metabolism and stress tolerance traits that allow the bacterium to cope with different environmental conditions. In this work, the mechanisms that allow P. putida KT2440 to grow in the presence of four sole carbon sources (glucose, citrate, ferulic acid, serine) were investigated by RNA sequencing (RNA-seq) and genome-scale metabolic modelling. Transcriptomic data identified uptake systems for the four carbon sources, and candidates were subjected to preliminary experimental characterization by mutant strain growth to test their involvement in substrate assimilation. The OpdH and BenF-like porins were involved in citrate and ferulic acid uptake respectively. The citrate transporter (encoded by PP_0147) and the TctABC system were important for supporting cell growth in citrate; PcaT and VanK were associated with ferulic acid uptake; and the ABC transporter AapJPQM was involved in serine transport. A genome-scale metabolic model of P. putida KT2440 was used to integrate and analyze the transcriptomic data, identifying and confirming the active catabolic pathways for each carbon source. This study reveals novel information about transporters that are essential for understanding bacterial adaptation to different environments.
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Affiliation(s)
- Isotta D'Arrigo
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, DK-2800, Kongens Lyngby, Denmark
| | - João G R Cardoso
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, DK-2800, Kongens Lyngby, Denmark
| | - Maja Rennig
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, DK-2800, Kongens Lyngby, Denmark
| | - Nikolaus Sonnenschein
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, DK-2800, Kongens Lyngby, Denmark
| | - Markus J Herrgård
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, DK-2800, Kongens Lyngby, Denmark
| | - Katherine S Long
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, DK-2800, Kongens Lyngby, Denmark
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20
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Poblete-Castro I, Wittmann C, Nikel PI. Biochemistry, genetics and biotechnology of glycerol utilization in Pseudomonas species. Microb Biotechnol 2019; 13:32-53. [PMID: 30883020 PMCID: PMC6922529 DOI: 10.1111/1751-7915.13400] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 02/17/2019] [Accepted: 02/23/2019] [Indexed: 11/30/2022] Open
Abstract
The use of renewable waste feedstocks is an environment‐friendly choice contributing to the reduction of waste treatment costs and increasing the economic value of industrial by‐products. Glycerol (1,2,3‐propanetriol), a simple polyol compound widely distributed in biological systems, constitutes a prime example of a relatively cheap and readily available substrate to be used in bioprocesses. Extensively exploited as an ingredient in the food and pharmaceutical industries, glycerol is also the main by‐product of biodiesel production, which has resulted in a progressive drop in substrate price over the years. Consequently, glycerol has become an attractive substrate in biotechnology, and several chemical commodities currently produced from petroleum have been shown to be obtained from this polyol using whole‐cell biocatalysts with both wild‐type and engineered bacterial strains. Pseudomonas species, endowed with a versatile and rich metabolism, have been adopted for the conversion of glycerol into value‐added products (ranging from simple molecules to structurally complex biopolymers, e.g. polyhydroxyalkanoates), and a number of metabolic engineering strategies have been deployed to increase the number of applications of glycerol as a cost‐effective substrate. The unique genetic and metabolic features of glycerol‐grown Pseudomonas are presented in this review, along with relevant examples of bioprocesses based on this substrate – and the synthetic biology and metabolic engineering strategies implemented in bacteria of this genus aimed at glycerol valorization.
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Affiliation(s)
- Ignacio Poblete-Castro
- Biosystems Engineering Laboratory, Center for Bioinformatics and Integrative Biology, Faculty of Natural Sciences, Universidad Andrés Bello, Santiago de Chile, Chile
| | - Christoph Wittmann
- Institute of Systems Biotechnology, Universität des Saarlandes, Saarbrücken, Germany
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs Lyngby, Denmark
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21
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Kim J, Goñi‐Moreno A, Calles B, de Lorenzo V. Spatial organization of the gene expression hardware in
Pseudomonas putida. Environ Microbiol 2019; 21:1645-1658. [DOI: 10.1111/1462-2920.14544] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Revised: 12/09/2018] [Accepted: 01/23/2019] [Indexed: 12/11/2022]
Affiliation(s)
| | | | - Belén Calles
- Systems Biology ProgramCentro Nacional de Biotecnología‐CSIC, Campus de Cantoblanco Madrid, 28049 Spain
| | - Víctor de Lorenzo
- Systems Biology ProgramCentro Nacional de Biotecnología‐CSIC, Campus de Cantoblanco Madrid, 28049 Spain
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22
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Calero P, Nikel PI. Chasing bacterial chassis for metabolic engineering: a perspective review from classical to non-traditional microorganisms. Microb Biotechnol 2019; 12:98-124. [PMID: 29926529 PMCID: PMC6302729 DOI: 10.1111/1751-7915.13292] [Citation(s) in RCA: 143] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Revised: 05/28/2018] [Accepted: 05/29/2018] [Indexed: 12/27/2022] Open
Abstract
The last few years have witnessed an unprecedented increase in the number of novel bacterial species that hold potential to be used for metabolic engineering. Historically, however, only a handful of bacteria have attained the acceptance and widespread use that are needed to fulfil the needs of industrial bioproduction - and only for the synthesis of very few, structurally simple compounds. One of the reasons for this unfortunate circumstance has been the dearth of tools for targeted genome engineering of bacterial chassis, and, nowadays, synthetic biology is significantly helping to bridge such knowledge gap. Against this background, in this review, we discuss the state of the art in the rational design and construction of robust bacterial chassis for metabolic engineering, presenting key examples of bacterial species that have secured a place in industrial bioproduction. The emergence of novel bacterial chassis is also considered at the light of the unique properties of their physiology and metabolism, and the practical applications in which they are expected to outperform other microbial platforms. Emerging opportunities, essential strategies to enable successful development of industrial phenotypes, and major challenges in the field of bacterial chassis development are also discussed, outlining the solutions that contemporary synthetic biology-guided metabolic engineering offers to tackle these issues.
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Affiliation(s)
- Patricia Calero
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of Denmark2800Kongens LyngbyDenmark
| | - Pablo I. Nikel
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of Denmark2800Kongens LyngbyDenmark
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23
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Corona F, Martínez JL, Nikel PI. The global regulator Crc orchestrates the metabolic robustness underlying oxidative stress resistance in Pseudomonas aeruginosa. Environ Microbiol 2018; 21:898-912. [PMID: 30411469 DOI: 10.1111/1462-2920.14471] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Revised: 11/01/2018] [Accepted: 11/03/2018] [Indexed: 11/26/2022]
Abstract
The remarkable metabolic versatility of bacteria of the genus Pseudomonas enable their survival across very diverse environmental conditions. P. aeruginosa, one of the most relevant opportunistic pathogens, is a prime example of this adaptability. The interplay between regulatory networks that mediate these metabolic and physiological features is just starting to be explored in detail. Carbon catabolite repression, governed by the Crc protein, controls the availability of several enzymes and transporters involved in the assimilation of secondary carbon sources. Yet, the regulation exerted by Crc on redox metabolism of P. aeruginosa (hence, on the overall physiology) had hitherto been unexplored. In this study, we address the intimate connection between carbon catabolite repression and metabolic robustness of P. aeruginosa PAO1. In particular, we explored the interplay between oxidative stress, metabolic rearrangements in central carbon metabolism and the cellular redox state. By adopting a combination of quantitative physiology experiments, multiomic analyses, transcriptional patterns of key genes, measurement of metabolic activities in vitro and direct quantification of redox balances both in the wild-type strain and in an isogenic Δcrc derivative, we demonstrate that Crc orchestrates the overall response of P. aeruginosa to oxidative stress via reshaping of the core metabolic architecture in this bacterium.
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Affiliation(s)
- Fernando Corona
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología (CNB-CSIC), 28049 Madrid, Spain
| | - José Luis Martínez
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología (CNB-CSIC), 28049 Madrid, Spain
| | - Pablo I Nikel
- Systems Environmental Microbiology Group, The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs Lyngby, Denmark
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24
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Pérez‐Pantoja D, Kim J, Platero R, de Lorenzo V. The interplay of EIIANtrwith C‐source regulation of thePupromoter ofPseudomonas putidamt‐2. Environ Microbiol 2018; 20:4555-4566. [DOI: 10.1111/1462-2920.14410] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 09/04/2018] [Accepted: 09/09/2018] [Indexed: 11/29/2022]
Affiliation(s)
- Danilo Pérez‐Pantoja
- Programa Institucional de Fomento a la Investigación, Desarrollo e InnovaciónUniversidad Tecnológica Metropolitana Ignacio Valdivieso 2409, San Joaquín, Santiago Chile
| | - Juhyun Kim
- Systems Biology ProgramCentro Nacional de Biotecnología‐CSIC Campus de Cantoblanco, Madrid 28049 Spain
| | - Raúl Platero
- Systems Biology ProgramCentro Nacional de Biotecnología‐CSIC Campus de Cantoblanco, Madrid 28049 Spain
| | - Víctor de Lorenzo
- Systems Biology ProgramCentro Nacional de Biotecnología‐CSIC Campus de Cantoblanco, Madrid 28049 Spain
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25
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Simeoni M, Citraro ML, Cerantonio A, Deodato F, Provenzano M, Cianfrone P, Capria M, Corrado S, Libri E, Comi A, Pujia A, Abenavoli L, Andreucci M, Cocchi M, Montalcini T, Fuiano G. An open-label, randomized, placebo-controlled study on the effectiveness of a novel probiotics administration protocol (ProbiotiCKD) in patients with mild renal insufficiency (stage 3a of CKD). Eur J Nutr 2018; 58:2145-2156. [PMID: 30076458 PMCID: PMC6647244 DOI: 10.1007/s00394-018-1785-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 07/17/2018] [Indexed: 12/16/2022]
Abstract
Purpose Gut dysbiosis has been described in advanced, but not in initial stages of CKD. Considering the relevant impact of gut dysbiosis on renal and cardiovascular risk, its diagnosis and treatment are clinically relevant. Methods We designed, open-label, placebo-controlled intervention study (ProbiotiCKD) to evaluate gut microbiota metabolism in a cohort of KDIGO CKD patients (n = 28) at baseline and after a randomly assigned treatment with probiotics or placebo. Gut microbiota status was evaluated on:. Results Basal mean fecal Lactobacillales and Bifidobacteria concentrations were abnormally low in both groups, while urinary indican and 3-MI levels were, indicating a mixed (fermentative and putrefactive) dysbiosis. After treatment, mean fecal Lactobacillales and Bifidobacteria concentrations were increased, only in the probiotics group (p < 0.001). Conversely, mean urinary indican and 3-MI levels only in the group treated with probiotics (p < 0.001). Compared to placebo group, significant improvements of C-reactive protein (p < 0.001), iron (p < 0.001), ferritin (p < 0.001), transferrin saturation (p < 0.001), β2-microglobulin (p < 0.001), serum iPTH and serum calcium were observed only in the probiotics group. Conclusions ProbiotiCKD is the first intervention study demonstrating that an intestinal mixed dysbiosis is present even in early CKD stage and can be effectively corrected by the novel mode of administration of high-quality probiotics with improvement of inflammatory indices, iron status and iPTH stabilization.
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Affiliation(s)
- Mariadelina Simeoni
- Nephrology Unit, Department of Surgical and Medical Science, 'Magna Graecia' University Hospital, Viale Europa, Germaneto Area, 88100, Catanzaro, CZ, Italy.
| | - Maria Lucia Citraro
- Nephrology Unit, Department of Surgical and Medical Science, 'Magna Graecia' University Hospital, Viale Europa, Germaneto Area, 88100, Catanzaro, CZ, Italy
| | - Annamaria Cerantonio
- Nephrology Unit, Department of Surgical and Medical Science, 'Magna Graecia' University Hospital, Viale Europa, Germaneto Area, 88100, Catanzaro, CZ, Italy
| | - Francesca Deodato
- Nephrology Unit, Department of Surgical and Medical Science, 'Magna Graecia' University Hospital, Viale Europa, Germaneto Area, 88100, Catanzaro, CZ, Italy
| | - Michele Provenzano
- Nephrology Unit, Department of Surgical and Medical Science, 'Magna Graecia' University Hospital, Viale Europa, Germaneto Area, 88100, Catanzaro, CZ, Italy
| | - Paola Cianfrone
- Nephrology Unit, Department of Surgical and Medical Science, 'Magna Graecia' University Hospital, Viale Europa, Germaneto Area, 88100, Catanzaro, CZ, Italy
| | - Maria Capria
- Nephrology Unit, Department of Surgical and Medical Science, 'Magna Graecia' University Hospital, Viale Europa, Germaneto Area, 88100, Catanzaro, CZ, Italy
| | - Silvia Corrado
- Nephrology Unit, Department of Surgical and Medical Science, 'Magna Graecia' University Hospital, Viale Europa, Germaneto Area, 88100, Catanzaro, CZ, Italy
| | - Emanuela Libri
- Nephrology Unit, Department of Surgical and Medical Science, 'Magna Graecia' University Hospital, Viale Europa, Germaneto Area, 88100, Catanzaro, CZ, Italy
| | - Alessandro Comi
- Nephrology Unit, Department of Surgical and Medical Science, 'Magna Graecia' University Hospital, Viale Europa, Germaneto Area, 88100, Catanzaro, CZ, Italy
| | - Arturo Pujia
- Clinical Nutrition Unit, 'Magna Graecia' University Hospital, 88100, Catanzaro, CZ, Italy
| | - Ludovico Abenavoli
- Digestive Physiopathology Unit, 'Magna Graecia' University Hospital, 88100, Catanzaro, CZ, Italy
| | - Michele Andreucci
- Nephrology Unit, Department of Surgical and Medical Science, 'Magna Graecia' University Hospital, Viale Europa, Germaneto Area, 88100, Catanzaro, CZ, Italy
| | - Massimo Cocchi
- "Paolo Sotgiu" Institute for Research in Quantitative and Quantum Psychiatry and Cardiology, LUdeS, Lugano, Switzerland
| | - Tiziana Montalcini
- Clinical Nutrition Unit, 'Magna Graecia' University Hospital, 88100, Catanzaro, CZ, Italy
| | - Giorgio Fuiano
- Nephrology Unit, Department of Surgical and Medical Science, 'Magna Graecia' University Hospital, Viale Europa, Germaneto Area, 88100, Catanzaro, CZ, Italy
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26
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Houghton D, Hardy T, Stewart C, Errington L, Day CP, Trenell MI, Avery L. Systematic review assessing the effectiveness of dietary intervention on gut microbiota in adults with type 2 diabetes. Diabetologia 2018; 61:1700-1711. [PMID: 29754286 PMCID: PMC6061157 DOI: 10.1007/s00125-018-4632-0] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 03/05/2018] [Indexed: 12/27/2022]
Abstract
AIMS/HYPOTHESIS Despite improved understanding of the pathophysiology of type 2 diabetes mellitus, explanations for individual variability in disease progression and response to treatment are incomplete. The gut microbiota has been linked to the pathophysiology of type 2 diabetes mellitus and may account for this variability. We conducted a systematic review to assess the effectiveness of dietary and physical activity/exercise interventions in modulating the gut microbiota and improving glucose control in adults with type 2 diabetes mellitus. METHODS A systematic search was conducted to identify studies reporting on the effect of dietary and physical activity/exercise interventions on the gut microbiota and glucose control in individuals with a confirmed diagnosis of type 2 diabetes mellitus. Study characteristics, methodological quality and details relating to interventions were captured using a data-extraction form. Meta-analyses were conducted where sufficient data were available, and other results were reported narratively. RESULTS Eight studies met the eligibility criteria of the systematic review. No studies were found that reported on the effects of physical activity/exercise on the gut microbiota and glucose control. However, studies reporting on dietary interventions showed that such interventions were associated with modifications to the composition and diversity of the gut microbiota. There was a statistically significant improvement in HbA1c (standardised mean difference [SMD] -2.31 mmol/mol [95% CI -2.76, -1.85] [0.21%; 95% CI -0.26, -0.16]; I2 = 0%, p < 0.01), but not in fasting blood glucose (SMD -0.25 mmol/l [95% CI -0.85, 0.35], I2 = 87%, p > 0.05), fasting insulin (SMD -1.82 pmol/l [95% CI -7.23, 3.60], I2 = 54%, p > 0.05) or HOMA-IR (SMD -0.15 [95% CI -0.63, 0.32], I2 = 69%, p > 0.05) when comparing dietary interventions with comparator groups. There were no significant changes in the relative abundance of bacteria in the genera Bifidobacterium (SMD 1.29% [95% CI -4.45, 7.03], I2 = 33%, p > 0.05), Roseburia (SMD -0.85% [95% CI -2.91, 1.21], I2 = 79%, p > 0.05) or Lactobacillus (SMD 0.04% [95% CI -0.01, 0.09], I2 = 0%, p > 0.05) when comparing dietary interventions with comparator groups. There were, however, other significant changes in the gut microbiota, including changes at various taxonomic levels, including phylum, family, genus and species, Firmicutes:Bacteroidetes ratios and changes in diversity matrices (α and β). Dietary intervention had minimal or no effect on inflammation, short-chain fatty acids or anthropometrics. CONCLUSIONS/INTERPRETATION Dietary intervention was found to modulate the gut microbiota and improve glucose control in individuals with type 2 diabetes. Although the results of the included studies are encouraging, this review highlights the need for further well-conducted interventional studies to inform the clinical use of dietary interventions targeting the gut microbiota.
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Affiliation(s)
- David Houghton
- Institute of Cellular Medicine, 4th Floor William Leech Building, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.
| | - Timothy Hardy
- Institute of Cellular Medicine, 4th Floor William Leech Building, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
- Liver Unit, Freeman Hospital, Newcastle Upon Tyne Hospitals NHS Trust, Newcastle Upon Tyne, UK
| | - Christopher Stewart
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Linda Errington
- Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Christopher P Day
- Institute of Cellular Medicine, 4th Floor William Leech Building, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
- Liver Unit, Freeman Hospital, Newcastle Upon Tyne Hospitals NHS Trust, Newcastle Upon Tyne, UK
| | - Michael I Trenell
- Institute of Cellular Medicine, 4th Floor William Leech Building, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Leah Avery
- Institute of Cellular Medicine, 4th Floor William Leech Building, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
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Peng J, Miao L, Chen X, Liu P. Comparative Transcriptome Analysis of Pseudomonas putida KT2440 Revealed Its Response Mechanisms to Elevated Levels of Zinc Stress. Front Microbiol 2018; 9:1669. [PMID: 30087671 PMCID: PMC6066579 DOI: 10.3389/fmicb.2018.01669] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 07/04/2018] [Indexed: 01/03/2023] Open
Abstract
The whole-genome transcriptional response of Pseudomonas putida KT2440 to stress-inducing concentrations of zinc was analyzed in this study by RNA sequencing to thoroughly investigate the bacterial cell response to zinc toxicity. The data revealed that different levels of zinc stress strongly affected the transcription of genes from the following categories: metal transport genes, genes involved in membrane homeostasis, oxidative-stress-responding genes, and genes associated with basic cellular metabolism. At the lowest zinc dose, only several genes associated with metal transport and membrane homeostasis were strongly influenced. At the intermediate zinc dose, transcriptional changes of genes belonging to these two categories were highly pronounced. In addition, the intermediate zinc stress produced high levels of oxidative stress, and influenced amino acid metabolism and respiratory chains of P. putida. At the highest zinc dose, the induction of genes responsible for Fe–S cluster biogenesis was the most remarkable feature. Moreover, upregulation of glyoxylate cycle was observed. In summary, the adaptation of the cell envelope, the maintenance of metal homeostasis and intracellular redox status, and the transcriptional control of metabolism are the main elements of stress response, which facilitates the survival of P. putida KT2440 in zinc-polluted environments.
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Affiliation(s)
- Jun Peng
- College of Biological and Pharmaceutical Engineering, Wuhan Polytechnic University, Wuhan, China
| | - Lihong Miao
- College of Biological and Pharmaceutical Engineering, Wuhan Polytechnic University, Wuhan, China
| | - Xi Chen
- Wuhan Institute of Virology, Chinese Academy of Science, Wuhan, China
| | - Pulin Liu
- College of Biological and Pharmaceutical Engineering, Wuhan Polytechnic University, Wuhan, China
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28
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Volke DC, Nikel PI. Getting Bacteria in Shape: Synthetic Morphology Approaches for the Design of Efficient Microbial Cell Factories. ACTA ACUST UNITED AC 2018. [DOI: 10.1002/adbi.201800111] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Daniel C. Volke
- The Novo Nordisk Foundation Center for Biosustainability; Technical University of Denmark; Kemitorvet 2800 Kgs. Lyngby Denmark
| | - Pablo I. Nikel
- The Novo Nordisk Foundation Center for Biosustainability; Technical University of Denmark; Kemitorvet 2800 Kgs. Lyngby Denmark
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29
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Sánchez-Pascuala A, Nikel PI, de Lorenzo V. Re-Factoring Glycolytic Genes for Targeted Engineering of Catabolism in Gram-Negative Bacteria. Methods Mol Biol 2018; 1772:3-24. [PMID: 29754220 DOI: 10.1007/978-1-4939-7795-6_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2023]
Abstract
The Embden-Meyerhof-Parnas (EMP) pathway is widely accepted to be the biochemical standard of glucose catabolism. The well-characterized glycolytic route of Escherichia coli, based on the EMP catabolism, is an example of an intricate pathway in terms of genomic organization of the genes involved and patterns of gene expression and regulation. This intrinsic genetic and metabolic complexity renders it difficult to engineer glycolytic activities and transfer them onto other microbial cell factories, thus limiting the biotechnological potential of bacterial hosts that lack the route. Taking into account the potential applications of such a portable tool for targeted pathway engineering, in the present protocol we describe how the genes encoding all the enzymes of the linear EMP route have been individually recruited from the genome of E. coli K-12, edited in silico to remove their endogenous regulatory signals, and synthesized de novo following a standard (i.e., GlucoBrick) that facilitates their grouping in the form of functional modules that can be combined at the user's will. This novel genetic tool allows for the à la carte implementation or boosting of EMP pathway activities into different Gram-negative bacteria. The potential of the GlucoBrick platform is further illustrated by engineering novel glycolytic activities in the most representative members of the Pseudomonas genus (Pseudomonas putida and Pseudomonas aeruginosa).
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Affiliation(s)
| | - Pablo I Nikel
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
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30
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Whon TW, Chung WH, Lim MY, Song EJ, Kim PS, Hyun DW, Shin NR, Bae JW, Nam YD. The effects of sequencing platforms on phylogenetic resolution in 16 S rRNA gene profiling of human feces. Sci Data 2018; 5:180068. [PMID: 29688220 PMCID: PMC5914283 DOI: 10.1038/sdata.2018.68] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 02/27/2018] [Indexed: 12/11/2022] Open
Abstract
High-quality and high-throughput sequencing technologies are required for therapeutic and diagnostic analyses of human gut microbiota. Here, we evaluated the advantages and disadvantages of the various commercial sequencing platforms for studying human gut microbiota. We generated fecal bacterial sequences from 170 Korean subjects using the GS FLX+ (V1–4), Illumina MiSeq (V1–3, V3–4 and V4), and PacBio (V1–9) systems. Comparative analyses revealed that the PacBio data showed the weakest relationship with the reference whole-metagenome shotgun datasets. The PacBio system generated sequences with a significantly higher level of deletions than datasets generated by other platforms, with an abnormally high proportion of sequences assigned to the phylum Proteobacteria. Low sequencing accuracy and low coverage of terminal regions in public 16 S rRNA databases deteriorate the advantages of long read length, resulting in low taxonomic resolution in amplicon sequencing of human gut microbiota.
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Affiliation(s)
- Tae Woong Whon
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Won-Hyong Chung
- Research Group of Gut Microbiome, Division of Nutrition and Metabolism Research, Korea Food Research Institute, Sungnam 463-746, Republic of Korea
| | - Mi Young Lim
- Research Group of Gut Microbiome, Division of Nutrition and Metabolism Research, Korea Food Research Institute, Sungnam 463-746, Republic of Korea
| | - Eun-Ji Song
- Research Group of Gut Microbiome, Division of Nutrition and Metabolism Research, Korea Food Research Institute, Sungnam 463-746, Republic of Korea.,Korea University of Science and Technology, Daejeon 305-350, Republic of Korea
| | - Pil Soo Kim
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Dong-Wook Hyun
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Na-Ri Shin
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Jin-Woo Bae
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Young-Do Nam
- Research Group of Gut Microbiome, Division of Nutrition and Metabolism Research, Korea Food Research Institute, Sungnam 463-746, Republic of Korea.,Korea University of Science and Technology, Daejeon 305-350, Republic of Korea
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Nikel PI, de Lorenzo V. Assessing Carbon Source-Dependent Phenotypic Variability in Pseudomonas putida. Methods Mol Biol 2018; 1745:287-301. [PMID: 29476475 DOI: 10.1007/978-1-4939-7680-5_16] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The soil bacterium Pseudomonas putida is rapidly becoming a platform of choice for applications that require a microbial host highly resistant to different types of stresses and elevated rates of reducing power regeneration. P. putida is capable of growing in a wide variety of carbon sources that range from simple sugars to complex substrates such as aromatic compounds. Interestingly, the growth of the reference strain KT2440 on glycerol as the sole carbon source is characterized by a prolonged lag phase, not observed with other carbon substrates. This macroscopic phenomenon has been shown to be connected with the stochastic expression of the glp genes, which encode the enzymes needed for glycerol processing. In this protocol, we propose a general procedure to examine bacterial growth in small-scale cultures while monitoring the metabolic activity of individual cells. Assessing the metabolic capacity of single bacteria by means of fluorescence microscopy and flow cytometry, in combination with the analysis of the temporal takeoff of growth in single-cell cultures, is a simple and easy-to-implement approach. It can help to understand the link between macroscopic phenotypes (e.g., microbial growth in batch cultures) and stochastic phenomena at the genetic level. The implementation of these methodologies revealed that the adoption of a glycerol-metabolizing regime by P. putida KT2440 is not the result of a gradual change in the whole population, but it rather reflects a time-dependent bimodal switch between metabolically inactive (i.e., not growing) to fully active (i.e., growing) bacteria.
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Affiliation(s)
- Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Víctor de Lorenzo
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain.
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32
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Dvořák P, Nikel PI, Damborský J, de Lorenzo V. Bioremediation 3 . 0 : Engineering pollutant-removing bacteria in the times of systemic biology. Biotechnol Adv 2017; 35:845-866. [DOI: 10.1016/j.biotechadv.2017.08.001] [Citation(s) in RCA: 126] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Revised: 08/01/2017] [Accepted: 08/04/2017] [Indexed: 01/07/2023]
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Serrano-Villar S, Vázquez-Castellanos JF, Vallejo A, Latorre A, Sainz T, Ferrando-Martínez S, Rojo D, Martínez-Botas J, Del Romero J, Madrid N, Leal M, Mosele JI, Motilva MJ, Barbas C, Ferrer M, Moya A, Moreno S, Gosalbes MJ, Estrada V. The effects of prebiotics on microbial dysbiosis, butyrate production and immunity in HIV-infected subjects. Mucosal Immunol 2017; 10:1279-1293. [PMID: 28000678 DOI: 10.1038/mi.2016.122] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 11/19/2016] [Indexed: 02/06/2023]
Abstract
Altered interactions between the gut mucosa and bacteria during HIV infection seem to contribute to chronic immune dysfunction. A deeper understanding of how nutritional interventions could ameliorate gut dysbiosis is needed. Forty-four subjects, including 12 HIV+ viremic untreated (VU) patients, 23 antiretroviral therapy-treated (ART+) virally suppressed patients (15 immunological responders and 8 non-responders) and 9 HIV- controls (HIV-), were blindly randomized to receive either prebiotics (scGOS/lcFOS/glutamine) or placebo (34/10) over 6 weeks in this pilot study. We assessed fecal microbiota composition using deep 16S rRNA gene sequencing and several immunological and genetic markers involved in HIV immunopathogenesis. The short dietary supplementation attenuated HIV-associated dysbiosis, which was most apparent in VU individuals but less so in ART+ subjects, whose gut microbiota was found more resilient. This compositional shift was not observed in the placebo arm. Significantly, declines in indirect markers of bacterial translocation and T-cell activation, improvement of thymic output, and changes in butyrate production were observed. Increases in the abundance of Faecalibacterium and Lachnospira strongly correlated with moderate but significant increases of butyrate production and amelioration of the inflammatory biomarkers soluble CD14 and high-sensitivity C-reactive protein, especially among VU. Hence, the bacterial butyrate synthesis pathway holds promise as a viable target for interventions.
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Affiliation(s)
- S Serrano-Villar
- Department of Infectious Diseases, Hospital Universitario Ramón y Cajal, Facultad de Medicina, Universidad de Alcalá (IRYCIS), Madrid, Spain
| | - J F Vázquez-Castellanos
- Unidad Mixta de Investigación en Genómica y Salud de la Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO-Salud Pública) y el Instituto Cavanilles de Biodiversidad y Biología Evolutiva (Universidad de Valencia), Valencia, Spain
- CIBER en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - A Vallejo
- Department of Infectious Diseases, Hospital Universitario Ramón y Cajal, Facultad de Medicina, Universidad de Alcalá (IRYCIS), Madrid, Spain
| | - A Latorre
- Unidad Mixta de Investigación en Genómica y Salud de la Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO-Salud Pública) y el Instituto Cavanilles de Biodiversidad y Biología Evolutiva (Universidad de Valencia), Valencia, Spain
- CIBER en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - T Sainz
- Department of Pediatric Infectious Diseases, University Hospital La Paz, and La Paz Research Institute, Madrid, Spain
| | - S Ferrando-Martínez
- Laboratory of Immunovirology, Biomedicine Institute of Seville (IBIS), Department of Infectious Diseases, University Hospital Virgen del Rocío, Sevilla, Spain
| | - D Rojo
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, CEU San Pablo University, Madrid, Spain
| | - J Martínez-Botas
- Department of Biochemistry, University Hospital Ramón y Cajal-IRYCIS, Madrid, Spain
- CIBER of Obesity and Nutrition Pathophysiology (CIBEROBN), Madrid, Spain
| | | | - N Madrid
- Department of Infectious Diseases, Hospital Universitario Ramón y Cajal, Facultad de Medicina, Universidad de Alcalá (IRYCIS), Madrid, Spain
| | - M Leal
- Laboratory of Immunovirology, Biomedicine Institute of Seville (IBIS), Department of Infectious Diseases, University Hospital Virgen del Rocío, Sevilla, Spain
| | - J I Mosele
- Food Technology Department, Agrotecnio Center, University of Lleida, Spain
| | - M J Motilva
- Food Technology Department, Agrotecnio Center, University of Lleida, Spain
| | - C Barbas
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, CEU San Pablo University, Madrid, Spain
| | - M Ferrer
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - A Moya
- Unidad Mixta de Investigación en Genómica y Salud de la Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO-Salud Pública) y el Instituto Cavanilles de Biodiversidad y Biología Evolutiva (Universidad de Valencia), Valencia, Spain
- CIBER en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - S Moreno
- Department of Infectious Diseases, Hospital Universitario Ramón y Cajal, Facultad de Medicina, Universidad de Alcalá (IRYCIS), Madrid, Spain
| | - M J Gosalbes
- Unidad Mixta de Investigación en Genómica y Salud de la Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO-Salud Pública) y el Instituto Cavanilles de Biodiversidad y Biología Evolutiva (Universidad de Valencia), Valencia, Spain
- CIBER en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - V Estrada
- HIV Unit, Department of Internal Medicine, University Hospital Clínico San Carlos, Madrid, Spain
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Sánchez-Pascuala A, de Lorenzo V, Nikel PI. Refactoring the Embden-Meyerhof-Parnas Pathway as a Whole of Portable GlucoBricks for Implantation of Glycolytic Modules in Gram-Negative Bacteria. ACS Synth Biol 2017; 6:793-805. [PMID: 28121421 PMCID: PMC5440799 DOI: 10.1021/acssynbio.6b00230] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
The
Embden–Meyerhof–Parnas (EMP) pathway is generally
considered to be the biochemical standard for glucose catabolism.
Alas, its native genomic organization and the control of gene expression
in Escherichia coli are both very intricate, which
limits the portability of the EMP pathway to other biotechnologically
important bacterial hosts that lack the route. In this work, the genes
encoding all the enzymes of the linear EMP route have been individually
recruited from the genome of E. coli K-12, edited in silico to remove their endogenous regulatory signals,
and synthesized de novo following a standard (GlucoBrick)
that enables their grouping in the form of functional modules at the
user’s will. After verifying their activity in several glycolytic
mutants of E. coli, the versatility of these
GlucoBricks was demonstrated in quantitative physiology tests and
biochemical assays carried out in Pseudomonas putida KT2440 and P. aeruginosa PAO1 as the heterologous
hosts. Specific configurations of GlucoBricks were also adopted to
streamline the downward circulation of carbon from hexoses to pyruvate
in E. coli recombinants, thereby resulting in
a 3-fold increase of poly(3-hydroxybutyrate) synthesis from glucose.
Refactoring whole metabolic blocks in the fashion described in this
work thus eases the engineering of biochemical processes where the
optimization of carbon traffic is facilitated by the operation of
the EMP pathway—which yields more ATP than other glycolytic
routes such as the Entner–Doudoroff pathway.
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Affiliation(s)
- Alberto Sánchez-Pascuala
- Systems and Synthetic Biology
Program, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain
| | - Víctor de Lorenzo
- Systems and Synthetic Biology
Program, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain
| | - Pablo I. Nikel
- Systems and Synthetic Biology
Program, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain
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Singh RK, Chang HW, Yan D, Lee KM, Ucmak D, Wong K, Abrouk M, Farahnik B, Nakamura M, Zhu TH, Bhutani T, Liao W. Influence of diet on the gut microbiome and implications for human health. J Transl Med 2017; 15:73. [PMID: 28388917 PMCID: PMC5385025 DOI: 10.1186/s12967-017-1175-y] [Citation(s) in RCA: 1358] [Impact Index Per Article: 194.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 03/21/2017] [Indexed: 02/06/2023] Open
Abstract
Recent studies have suggested that the intestinal microbiome plays an important role in modulating risk of several chronic diseases, including inflammatory bowel disease, obesity, type 2 diabetes, cardiovascular disease, and cancer. At the same time, it is now understood that diet plays a significant role in shaping the microbiome, with experiments showing that dietary alterations can induce large, temporary microbial shifts within 24 h. Given this association, there may be significant therapeutic utility in altering microbial composition through diet. This review systematically evaluates current data regarding the effects of several common dietary components on intestinal microbiota. We show that consumption of particular types of food produces predictable shifts in existing host bacterial genera. Furthermore, the identity of these bacteria affects host immune and metabolic parameters, with broad implications for human health. Familiarity with these associations will be of tremendous use to the practitioner as well as the patient.
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Affiliation(s)
- Rasnik K. Singh
- University of California, Los Angeles, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095 USA
| | - Hsin-Wen Chang
- Department of Dermatology, University of California, San Francisco, 2340 Sutter St. Room N431, Box 0808, San Francisco, CA 94115 USA
| | - Di Yan
- Department of Dermatology, University of California, San Francisco, 2340 Sutter St. Room N431, Box 0808, San Francisco, CA 94115 USA
| | - Kristina M. Lee
- Department of Dermatology, University of California, San Francisco, 2340 Sutter St. Room N431, Box 0808, San Francisco, CA 94115 USA
| | - Derya Ucmak
- Department of Dermatology, University of California, San Francisco, 2340 Sutter St. Room N431, Box 0808, San Francisco, CA 94115 USA
| | - Kirsten Wong
- Department of Dermatology, University of California, San Francisco, 2340 Sutter St. Room N431, Box 0808, San Francisco, CA 94115 USA
| | - Michael Abrouk
- University of California, Irvine, School of Medicine, Irvine, CA 92697 USA
| | | | - Mio Nakamura
- Department of Dermatology, University of California, San Francisco, 2340 Sutter St. Room N431, Box 0808, San Francisco, CA 94115 USA
| | - Tian Hao Zhu
- University of Southern California Keck School of Medicine, Los Angeles, CA 90033 USA
| | - Tina Bhutani
- Department of Dermatology, University of California, San Francisco, 2340 Sutter St. Room N431, Box 0808, San Francisco, CA 94115 USA
| | - Wilson Liao
- Department of Dermatology, University of California, San Francisco, 2340 Sutter St. Room N431, Box 0808, San Francisco, CA 94115 USA
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A Metabolic Widget Adjusts the Phosphoenolpyruvate-Dependent Fructose Influx in Pseudomonas putida. mSystems 2016; 1:mSystems00154-16. [PMID: 27933319 PMCID: PMC5141268 DOI: 10.1128/msystems.00154-16] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 11/01/2016] [Indexed: 12/22/2022] Open
Abstract
Fructose uptake in the soil bacterium Pseudomonas putida occurs through a canonical phosphoenolpyruvate (PEP)-dependent sugar transport system (PTSFru). The logic of the genetic circuit that rules its functioning is puzzling: the transcription of the fruBKA operon, encoding all the components of PTSFru, can escape the repression exerted by the catabolite repressor/activator protein Cra solely in the presence of intracellular fructose-1-P, an agonist formed only when fructose has been already transported. To study this apparently incongruous regulatory architecture, the changes in the transcriptome brought about by a seamless Δcra deletion in P. putida strain KT2440 were inspected under different culture conditions. The few genes found to be upregulated in the cra mutant unexpectedly included PP_3443, encoding a bona fide glyceraldehyde-3-P dehydrogenase. An in silico model was developed to explore emergent properties that could result from such connections between sugar uptake with Cra and PEP. Simulation of fructose transport revealed that sugar uptake called for an extra supply of PEP (obtained through the activity of PP_3443) that was kept (i.e., memorized) even when the carbohydrate disappeared from the medium. This feature was traced to the action of two sequential inverters that connect the availability of exogenous fructose to intracellular PEP levels via Cra/PP_3443. The loss of such memory caused a much longer lag phase in cells shifted from one growth condition to another. The term "metabolic widget" is proposed to describe a merged biochemical and regulatory patch that tailors a given node of the cell molecular network to suit species-specific physiological needs. IMPORTANCE The regulatory nodes that govern metabolic traffic in bacteria often show connectivities that could be deemed unnecessarily complex at a first glance. Being a soil dweller and plant colonizer, Pseudomonas putida frequently encounters fructose in the niches that it inhabits. As is the case with many other sugars, fructose is internalized by a dedicated phosphoenolpyruvate (PEP)-dependent transport system (PTSFru), the expression of which is repressed by the fructose-1-P-responding Cra regulatory protein. However, Cra also controls a glyceraldehyde-3-P dehydrogenase that fosters accumulation of PEP (i.e., the metabolic fuel for PTSFru). A simple model representing this metabolic and regulatory device revealed that such an unexpected connectivity allows cells to shift smoothly between fructose-rich and fructose-poor conditions. Therefore, although the metabolic networks that handle sugar (i.e., fructose) consumption look very similar in most eubacteria, the way in which their components are intertwined endows given microorganisms with emergent properties for meeting species-specific and niche-specific needs.
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Poblete-Castro I, Borrero-de Acuña JM, Nikel PI, Kohlstedt M, Wittmann C. Host Organism: Pseudomonas putida. Ind Biotechnol (New Rochelle N Y) 2016. [DOI: 10.1002/9783527807796.ch8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Ignacio Poblete-Castro
- Universidad Andrés Bello; Center for Bioinformatics and Integrative Biology, Biosystems Engineering Laboratory, Faculty of Biological Sciences; Av. República 239 8340176 Santiago de Chile Chile
| | - José M. Borrero-de Acuña
- Universidad Andrés Bello; Center for Bioinformatics and Integrative Biology, Biosystems Engineering Laboratory, Faculty of Biological Sciences; Av. República 239 8340176 Santiago de Chile Chile
| | - Pablo I. Nikel
- Systems and Synthetic Biology Program; National Spanish Center for Biotechnology (CNB-CSIC); Calle Darwin, 3 28049 Madrid, Spain
| | - Michael Kohlstedt
- Saarland University; Institute of Systems Biology, Biosciences; Campus A1.5 66123 Saarbrücken, Germany
| | - Christoph Wittmann
- Saarland University; Institute of Systems Biology, Biosciences; Campus A1.5 66123 Saarbrücken, Germany
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38
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Nikel PI, Pérez-Pantoja D, de Lorenzo V. Pyridine nucleotide transhydrogenases enable redox balance of Pseudomonas putida during biodegradation of aromatic compounds. Environ Microbiol 2016; 18:3565-3582. [PMID: 27348295 DOI: 10.1111/1462-2920.13434] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Accepted: 06/23/2016] [Indexed: 11/26/2022]
Abstract
The metabolic versatility of the soil bacterium Pseudomonas putida is reflected by its ability to execute strong redox reactions (e.g., mono- and di-oxygenations) on aromatic substrates. Biodegradation of aromatics occurs via the pathway encoded in the archetypal TOL plasmid pWW0, yet the effect of running such oxidative route on redox balance against the background metabolism of P. putida remains unexplored. To answer this question, the activity of pyridine nucleotide transhydrogenases (that catalyze the reversible interconversion of NADH and NADPH) was inspected under various physiological and oxidative stress regimes. The genome of P. putida KT2440 encodes a soluble transhydrogenase (SthA) and a membrane-bound, proton-pumping counterpart (PntAB). Mutant strains, lacking sthA and/or pntAB, were subjected to a panoply of genetic, biochemical, phenomic and functional assays in cells grown on customary carbon sources (e.g., citrate) versus difficult-to-degrade aromatic substrates. The results consistently indicated that redox homeostasis is compromised in the transhydrogenases-defective variant, rendering the mutant sensitive to oxidants. This metabolic deficiency was, however, counteracted by an increase in the activity of NADP+ -dependent dehydrogenases in central carbon metabolism. Taken together, these observations demonstrate that transhydrogenases enable a redox-adjusting mechanism that comes into play when biodegradation reactions are executed to metabolize unusual carbon compounds.
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Affiliation(s)
- Pablo I Nikel
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain
| | - Danilo Pérez-Pantoja
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain
- Department of Biochemistry and Molecular Biology, Faculty of Biological Sciences, University of Concepción, 4030000 Concepción, Chile
| | - Víctor de Lorenzo
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain.
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D'Arrigo I, Bojanovič K, Yang X, Holm Rau M, Long KS. Genome-wide mapping of transcription start sites yields novel insights into the primary transcriptome ofPseudomonas putida. Environ Microbiol 2016; 18:3466-3481. [DOI: 10.1111/1462-2920.13326] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 04/01/2016] [Indexed: 01/09/2023]
Affiliation(s)
- Isotta D'Arrigo
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark; Kogle Allé 6 DK-2970 Hørsholm Denmark
| | - Klara Bojanovič
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark; Kogle Allé 6 DK-2970 Hørsholm Denmark
| | - Xiaochen Yang
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark; Kogle Allé 6 DK-2970 Hørsholm Denmark
| | - Martin Holm Rau
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark; Kogle Allé 6 DK-2970 Hørsholm Denmark
| | - Katherine S. Long
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark; Kogle Allé 6 DK-2970 Hørsholm Denmark
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40
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Belda E, van Heck RGA, José Lopez-Sanchez M, Cruveiller S, Barbe V, Fraser C, Klenk HP, Petersen J, Morgat A, Nikel PI, Vallenet D, Rouy Z, Sekowska A, Martins dos Santos VAP, de Lorenzo V, Danchin A, Médigue C. The revisited genome ofPseudomonas putidaKT2440 enlightens its value as a robust metabolicchassis. Environ Microbiol 2016; 18:3403-3424. [DOI: 10.1111/1462-2920.13230] [Citation(s) in RCA: 217] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 01/16/2016] [Indexed: 01/08/2023]
Affiliation(s)
- Eugeni Belda
- Alternative Energies and Atomic Energy Commission (CEA), Genomic Institute & CNRS-UMR8030 & Evry University, Laboratory of Bioinformatics Analysis in Genomics and Metabolism; 2 rue Gaston Crémieux 91057 Evry France
- Institut Pasteur, Unit of Insect Vector Genetics and Genomics, Department of Parasitology and Mycology; 28, rue du Dr. Roux, Paris, Cedex 15 75724 France
| | - Ruben G. A. van Heck
- Laboratory of Systems and Synthetic Biology, Wageningen University; Dreijenplein 10, Building number 316 6703 HB Wageningen The Netherlands
| | - Maria José Lopez-Sanchez
- Alternative Energies and Atomic Energy Commission (CEA), Genomic Institute & CNRS-UMR8030 & Evry University, Laboratory of Bioinformatics Analysis in Genomics and Metabolism; 2 rue Gaston Crémieux 91057 Evry France
- AMAbiotics SAS, Institut du Cerveau et de la Moëlle Épinière, Hôpital de la Pitié-Salpêtrière; Paris France
| | - Stéphane Cruveiller
- Alternative Energies and Atomic Energy Commission (CEA), Genomic Institute & CNRS-UMR8030 & Evry University, Laboratory of Bioinformatics Analysis in Genomics and Metabolism; 2 rue Gaston Crémieux 91057 Evry France
| | - Valérie Barbe
- Alternative Energies and Atomic Energy Commission (CEA), Genomic Institute, National Sequencing Center; 2 rue Gaston Crémieux 91057 Evry France
| | - Claire Fraser
- Institute for Genome Sciences, Department of Microbiology and Immunology, University of Maryland School of Medicine; Baltimore MD USA
| | - Hans-Peter Klenk
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures; Braunschweig Germany
- School of Biology, Newcastle University; Newcastle upon Tyne NE1 7RU UK
| | - Jörn Petersen
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures; Braunschweig Germany
| | - Anne Morgat
- Swiss-Prot Group, SIB Swiss Institute of Bioinformatics; Geneva CH-1206 Switzerland
| | - Pablo I. Nikel
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología (CNB-CSIC); C/Darwin 3 28049 Madrid Spain
| | - David Vallenet
- Alternative Energies and Atomic Energy Commission (CEA), Genomic Institute & CNRS-UMR8030 & Evry University, Laboratory of Bioinformatics Analysis in Genomics and Metabolism; 2 rue Gaston Crémieux 91057 Evry France
| | - Zoé Rouy
- Alternative Energies and Atomic Energy Commission (CEA), Genomic Institute & CNRS-UMR8030 & Evry University, Laboratory of Bioinformatics Analysis in Genomics and Metabolism; 2 rue Gaston Crémieux 91057 Evry France
| | - Agnieszka Sekowska
- AMAbiotics SAS, Institut du Cerveau et de la Moëlle Épinière, Hôpital de la Pitié-Salpêtrière; Paris France
| | - Vitor A. P. Martins dos Santos
- Laboratory of Systems and Synthetic Biology, Wageningen University; Dreijenplein 10, Building number 316 6703 HB Wageningen The Netherlands
| | - Víctor de Lorenzo
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología (CNB-CSIC); C/Darwin 3 28049 Madrid Spain
| | - Antoine Danchin
- AMAbiotics SAS, Institut du Cerveau et de la Moëlle Épinière, Hôpital de la Pitié-Salpêtrière; Paris France
| | - Claudine Médigue
- Alternative Energies and Atomic Energy Commission (CEA), Genomic Institute & CNRS-UMR8030 & Evry University, Laboratory of Bioinformatics Analysis in Genomics and Metabolism; 2 rue Gaston Crémieux 91057 Evry France
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41
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Tamames J, Sánchez PD, Nikel PI, Pedrós-Alió C. Quantifying the Relative Importance of Phylogeny and Environmental Preferences As Drivers of Gene Content in Prokaryotic Microorganisms. Front Microbiol 2016; 7:433. [PMID: 27065987 PMCID: PMC4814473 DOI: 10.3389/fmicb.2016.00433] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Accepted: 03/17/2016] [Indexed: 01/15/2023] Open
Abstract
Two complementary forces shape microbial genomes: vertical inheritance of genes by phylogenetic descent, and acquisition of new genes related to adaptation to particular habitats and lifestyles. Quantification of the relative importance of each driving force proved difficult. We determined the contribution of each factor, and identified particular genes or biochemical/cellular processes linked to environmental preferences (i.e., propensity of a taxon to live in particular habitats). Three types of data were confronted: (i) complete genomes, which provide gene content of different taxa; (ii) phylogenetic information, via alignment of 16S rRNA sequences, which allowed determination of the distance between taxa, and (iii) distribution of species in environments via 16S rRNA sampling experiments, reflecting environmental preferences of different taxa. The combination of these three datasets made it possible to describe and quantify the relationships among them. We found that, although phylogenetic descent was responsible for shaping most genomes, a discernible part of the latter was correlated to environmental adaptations. Particular families of genes were identified as environmental markers, as supported by direct studies such as metagenomic sequencing. These genes are likely important for adaptation of bacteria to particular conditions or habitats, such as carbohydrate or glycan metabolism genes being linked to host-associated environments.
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Affiliation(s)
- Javier Tamames
- Departamento de Biología de Sistemas, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas Madrid, Spain
| | - Pablo D Sánchez
- Departamento de Biología de Sistemas, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas Madrid, Spain
| | - Pablo I Nikel
- Departamento de Biología de Sistemas, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas Madrid, Spain
| | - Carlos Pedrós-Alió
- Departamento de Biología de Sistemas, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones CientíficasMadrid, Spain; Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, Consejo Superior de Investigaciones CientíficasBarcelona, Spain
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42
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Gutiérrez-Díaz I, Fernández-Navarro T, Sánchez B, Margolles A, González S. Mediterranean diet and faecal microbiota: a transversal study. Food Funct 2016; 7:2347-56. [DOI: 10.1039/c6fo00105j] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The adherence to Mediterrean Diet pattern is associated with higher abundances of Bacteroidetes and lower of Firmicutes.
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Affiliation(s)
- I. Gutiérrez-Díaz
- Department of Functional Biology
- University of Oviedo
- 33006 Asturias
- Spain
- Department of Microbiology and Biochemistry of Dairy Products
| | | | - B. Sánchez
- Department of Microbiology and Biochemistry of Dairy Products
- Instituto de Productos Lácteos de Asturias - Consejo Superior de Investigaciones Científicas (IPLA-CSIC)
- 33300 Asturias
- Spain
| | - A. Margolles
- Department of Microbiology and Biochemistry of Dairy Products
- Instituto de Productos Lácteos de Asturias - Consejo Superior de Investigaciones Científicas (IPLA-CSIC)
- 33300 Asturias
- Spain
| | - S. González
- Department of Functional Biology
- University of Oviedo
- 33006 Asturias
- Spain
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43
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Ercolini D, Francavilla R, Vannini L, De Filippis F, Capriati T, Di Cagno R, Iacono G, De Angelis M, Gobbetti M. From an imbalance to a new imbalance: Italian-style gluten-free diet alters the salivary microbiota and metabolome of African celiac children. Sci Rep 2015; 5:18571. [PMID: 26681599 PMCID: PMC4683525 DOI: 10.1038/srep18571] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 11/20/2015] [Indexed: 02/08/2023] Open
Abstract
Fourteen Saharawi celiac children following an African-style gluten-free diet for at least two years were subjected to a change of diet to an Italian-style gluten-free diet for 60 days. Significant differences were identified in the salivary microbiota and metabolome when Saharawi celiac children switched from African- to Italian-style dietary habits. An Italian-style gluten-free diet caused increases in the abundance of Granulicatella, Porphyromonas and Neisseria and decreases in Clostridium, Prevotella and Veillonella, altering the ‘salivary type’ of the individuals. Furthermore, operational taxonomic unit co-occurrence/exclusion patterns indicated that the initial equilibrium of co-occurring microbial species was perturbed by a change in diet: the microbial diversity was reduced, with a few species out-competing the previously established microbiota and becoming dominant. Analysis of predicted metagenomes revealed a remarkable change in the metabolic potential of the microbiota following the diet change, with increased potential for amino acid, vitamin and co-factor metabolism. High concentrations of acetone and 2-butanone during treatment with the Italian-style gluten-free diet suggested metabolic dysfunction in the Saharawi celiac children. The findings of this study support the need for a translational medicine pipeline to examine interactions between food and microbiota when evaluating human development, nutritional needs and the impact and consequences of westernisation.
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Affiliation(s)
- Danilo Ercolini
- Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, Portici, 80055, Italy
| | - Ruggiero Francavilla
- Department of Interdisciplinary Medicine, University of Bari Aldo Moro, Bari, 70126, Italy
| | - Lucia Vannini
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, 40121, Italy.,Inter-departmental Centre for Industrial Agri-Food Research, University of Cesena, Cesena, 47521, Italy
| | - Francesca De Filippis
- Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, Portici, 80055, Italy
| | - Teresa Capriati
- Pediatric Gastroenterology, Di Cristina Children's Hospital, Palermo, 90134, Italy
| | - Raffaella Di Cagno
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Bari, 70126, Italy
| | - Giuseppe Iacono
- Pediatric Gastroenterology, Di Cristina Children's Hospital, Palermo, 90134, Italy
| | - Maria De Angelis
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Bari, 70126, Italy
| | - Marco Gobbetti
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Bari, 70126, Italy
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44
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Arce-Rodríguez A, Calles B, Nikel PI, de Lorenzo V. The RNA chaperone Hfq enables the environmental stress tolerance super-phenotype ofPseudomonas putida. Environ Microbiol 2015; 18:3309-3326. [DOI: 10.1111/1462-2920.13052] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 09/09/2015] [Accepted: 09/09/2015] [Indexed: 11/30/2022]
Affiliation(s)
- Alejandro Arce-Rodríguez
- Systems Biology Program; Centro Nacional de Biotecnología (CNB-CSIC); Campus de Cantoblanco Madrid 28049 Spain
| | - Belén Calles
- Systems Biology Program; Centro Nacional de Biotecnología (CNB-CSIC); Campus de Cantoblanco Madrid 28049 Spain
| | - Pablo I. Nikel
- Systems Biology Program; Centro Nacional de Biotecnología (CNB-CSIC); Campus de Cantoblanco Madrid 28049 Spain
| | - Víctor de Lorenzo
- Systems Biology Program; Centro Nacional de Biotecnología (CNB-CSIC); Campus de Cantoblanco Madrid 28049 Spain
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45
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Aron-Wisnewsky J, Clément K. The gut microbiome, diet, and links to cardiometabolic and chronic disorders. Nat Rev Nephrol 2015; 12:169-81. [PMID: 26616538 DOI: 10.1038/nrneph.2015.191] [Citation(s) in RCA: 219] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Cardiometabolic diseases (CMDs) have been associated with changes in the composition of the gut microbiota, with links between the host environment and microbiota identified in preclinical models. High-throughput sequencing technology has facilitated in-depth studies of the gut microbiota, bacterial-derived metabolites, and their association with CMDs. Such strategies have shown that patients with CMDs frequently exhibit enrichment or depletion of certain bacterial groups in their resident microbiota compared to healthy individuals. Furthermore, the ability to transfer resident gut microbiota from mice or humans into germ-free mouse models, or between human patients, has enabled researchers to characterize the causative role of the gut microbiota in CMDs. These approaches have helped identify that dietary intake of choline, which is metabolized by the gut microbiota, is associated with cardiovascular outcomes in mice and humans. Trimethylamine N-oxide (TMAO) - a metabolite derived from the gut microbiota - is also associated with poor cardiovascular outcomes in patients with cardiovascular disease and is elevated in patients with chronic kidney disease (CKD). TMAO might represent a biomarker that links the environment and microbiota with CKD. This Review summarizes data suggesting a link between the gut microbiota and derived metabolites with food intake patterns, metabolic alterations, and chronic CMDs.
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Affiliation(s)
- Judith Aron-Wisnewsky
- Institute of Cardiometabolism and Nutrition (ICAN), Assistance Publique-Hôpitaux de Paris, INSERM, Sorbonne Université, Paris 6, Pitié-Salpêtrière hospital, F-75013 Paris, France
| | - Karine Clément
- Institute of Cardiometabolism and Nutrition (ICAN), Assistance Publique-Hôpitaux de Paris, INSERM, Sorbonne Université, Paris 6, Pitié-Salpêtrière hospital, F-75013 Paris, France
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46
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Fu J, Sharma P, Spicer V, Krokhin OV, Zhang X, Fristensky B, Cicek N, Sparling R, Levin DB. Quantitative 'Omics Analyses of Medium Chain Length Polyhydroxyalkanaote Metabolism in Pseudomonas putida LS46 Cultured with Waste Glycerol and Waste Fatty Acids. PLoS One 2015; 10:e0142322. [PMID: 26544181 PMCID: PMC4636370 DOI: 10.1371/journal.pone.0142322] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 10/19/2015] [Indexed: 12/19/2022] Open
Abstract
Transcriptomes and proteomes of Pseudomonas putida LS46 cultured with biodiesel-derived waste glycerol or waste free fatty acids, as sole carbon sources, were compared under conditions that were either permissive or non-permissive for synthesis of medium chain length polyhydroxyalkanoates (mcl-PHA). The objectives of this study were to elucidate mechanisms that influence activation of biopolymer synthesis, intra-cellular accumulation, and monomer composition, and determine if these were physiologically specific to the carbon sources used for growth of P. putida LS46. Active mcl-PHA synthesis by P. putida LS46 was associated with high expression levels of key mcl-PHA biosynthesis genes and/or gene products including monomer-supplying proteins, PHA synthases, and granule-associated proteins. 'Omics data suggested that expression of these genes were regulated by different genetic mechanisms in P. putida LS46 cells in different physiological states, when cultured on the two waste carbon sources. Optimal polymer production by P. putida LS46 was primarily limited by less efficient glycerol metabolism during mcl-PHA synthesis on waste glycerol. Mapping the 'Omics data to the mcl-PHA biosynthetic pathway revealed significant variations in gene expression, primarily involved in: 1) glycerol transportation; 2) enzymatic reactions that recycle reducing equivalents and produce key mcl-PHA biosynthesis pathway intermediates (e.g. NADH/NADPH, acetyl-CoA). Active synthesis of mcl-PHAs was observed during exponential phase in cultures with waste free fatty acids, and was associated with the fatty acid beta-oxidation pathway. A putative Thioesterase in the beta-oxidation pathway that may regulate the level of fatty acid beta-oxidation intermediates, and thus carbon flux to mcl-PHA biosynthesis, was highly up-regulated. Finally, the data suggested that differences in expression of selected fatty acid metabolism and mcl-PHA monomer-supplying enzymes may play a role in determining the monomer composition of mcl-PHA polymers. Understanding the relationships between genome content, gene and gene product expression, and how these factors influence polymer synthesis, will aid in optimization of mcl-PHA production by P. putida LS46 using biodiesel waste streams.
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Affiliation(s)
- Jilagamazhi Fu
- Department of Biosystem Engineering, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Parveen Sharma
- Department of Biosystem Engineering, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Vic Spicer
- Department of Internal Medicine & Manitoba Centre for Proteomics and Systems Biology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Oleg V. Krokhin
- Department of Internal Medicine & Manitoba Centre for Proteomics and Systems Biology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Xiangli Zhang
- Department of Plant Science, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Brian Fristensky
- Department of Plant Science, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Nazim Cicek
- Department of Biosystem Engineering, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Richard Sparling
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - David. B. Levin
- Department of Biosystem Engineering, University of Manitoba, Winnipeg, Manitoba, Canada
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47
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Kim J, Pérez-Pantoja D, Silva-Rocha R, Oliveros JC, de Lorenzo V. High-resolution analysis of the m-xylene/toluene biodegradation subtranscriptome of Pseudomonas putida mt-2. Environ Microbiol 2015; 18:3327-3341. [PMID: 26373670 DOI: 10.1111/1462-2920.13054] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 08/30/2015] [Accepted: 09/12/2015] [Indexed: 11/28/2022]
Abstract
Pseudomonas putida mt-2 metabolizes m-xylene and other aromatic compounds through the enzymes encoded by the xyl operons of the TOL plasmid pWW0 along with other chromosomally encoded activities. Tiling arrays of densely overlapping oligonucleotides were designed to cover every gene involved in this process, allowing dissection of operon structures and exposing the interplay of plasmid and chromosomal functions. All xyl sequences were transcribed in response to aromatic substrates and the 3'-termini of both upper and lower mRNA operons extended beyond their coding regions, i.e. the 3'-end of the lower operon mRNA penetrated into the convergent xylS regulatory gene. Furthermore, xylR mRNA for the master m-xylene responsive regulator of the system was decreased by aromatic substrates, while the cognate upper operon mRNA was evenly stable throughout its full length. RNA sequencing confirmed these data at a single nucleotide level and refined the formerly misannotated xylL sequence. The chromosomal ortho route for degradation of benzoate (the ben, cat clusters and some pca genes) was activated by this aromatic, but not by the TOL substrates, toluene or m-xylene. We advocate this scenario as a testbed of natural retroactivity between a pre-existing metabolic network and a new biochemical pathway implanted through gene transfer.
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Affiliation(s)
- Juhyun Kim
- Systems Biology Program, Centro Nacional de Biotecnologia-CSIC, Campus de Cantoblanco, Madrid, Spain
| | - Danilo Pérez-Pantoja
- Systems Biology Program, Centro Nacional de Biotecnologia-CSIC, Campus de Cantoblanco, Madrid, Spain
| | - Rafael Silva-Rocha
- Systems Biology Program, Centro Nacional de Biotecnologia-CSIC, Campus de Cantoblanco, Madrid, Spain
| | - Juan Carlos Oliveros
- Systems Biology Program, Centro Nacional de Biotecnologia-CSIC, Campus de Cantoblanco, Madrid, Spain
| | - Víctor de Lorenzo
- Systems Biology Program, Centro Nacional de Biotecnologia-CSIC, Campus de Cantoblanco, Madrid, Spain.
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48
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Ramos JL, Sol Cuenca M, Molina-Santiago C, Segura A, Duque E, Gómez-García MR, Udaondo Z, Roca A. Mechanisms of solvent resistance mediated by interplay of cellular factors inPseudomonas putida. FEMS Microbiol Rev 2015; 39:555-66. [DOI: 10.1093/femsre/fuv006] [Citation(s) in RCA: 119] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/07/2015] [Indexed: 11/14/2022] Open
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49
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Páez-Espino AD, Chavarría M, de Lorenzo V. The two paralogue phoN (phosphinothricin acetyl transferase) genes of Pseudomonas putida encode functionally different proteins. Environ Microbiol 2015; 17:3330-40. [PMID: 25684119 DOI: 10.1111/1462-2920.12798] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Revised: 01/19/2015] [Accepted: 01/31/2015] [Indexed: 11/30/2022]
Abstract
Phosphinothricin (PPT) is a non-specific inhibitor of glutamine synthetase that has been employed as herbicide for selection of transgenic plants expressing cognate resistance genes. While the soil bacterium Pseudomonas putida KT2440 has been generally considered PPT-sensitive, inspection of its genome sequence reveals the presence of two highly similar open reading frames (PP_1924 and PP_4846) encoding acetylases with a potential to cause tolerance to the herbicide. To explore this possibility, each of these genes (named phoN1 and phoN2) was separately cloned and their activities examined in vivo and in vitro. Genetic and biochemical evidence indicated that phoN1 encodes a bona fide PPT-acetyl transferase, the expression of which suffices to make P. putida tolerant to high concentrations of the herbicide. In contrast, PhoN2 does not act on PPT but displays instead activity against methionine sulfoximine (MetSox), another glutamine synthetase inhibitor. When the geometry of the substrate-binding site of PhoN1 was grafted with the equivalent residues of the predicted PhoN2 structure, the resulting protein increased significantly MetSox resistance of the expression host concomitantly with the loss of activity on PPT. These observations uncover intricate biochemical and genetic interactions among soil microorganisms and how they can be perturbed by exposure to generic herbicides in soil.
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Affiliation(s)
- A David Páez-Espino
- Systems Biology Program, Centro Nacional de Biotecnología CSIC, Cantoblanco, Madrid, 28049, Spain
| | - Max Chavarría
- Systems Biology Program, Centro Nacional de Biotecnología CSIC, Cantoblanco, Madrid, 28049, Spain.,Escuela de Química, Universidad de Costa Rica, San José, 2060, Costa Rica
| | - Víctor de Lorenzo
- Systems Biology Program, Centro Nacional de Biotecnología CSIC, Cantoblanco, Madrid, 28049, Spain
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The glycerol-dependent metabolic persistence of Pseudomonas putida KT2440 reflects the regulatory logic of the GlpR repressor. mBio 2015; 6:mBio.00340-15. [PMID: 25827416 PMCID: PMC4453509 DOI: 10.1128/mbio.00340-15] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The growth of the soil bacterium Pseudomonas putida KT2440 on glycerol as the sole carbon source is characterized by a prolonged lag phase, not observed with other carbon substrates. We examined the bacterial growth in glycerol cultures while monitoring the metabolic activity of individual cells. Fluorescence microscopy and flow cytometry, as well as the analysis of the temporal start of growth in single-cell cultures, revealed that adoption of a glycerol-metabolizing regime was not the result of a gradual change in the whole population but rather reflected a time-dependent bimodal switch between metabolically inactive (i.e., nongrowing) and fully active (i.e., growing) bacteria. A transcriptional Φ(glpD-gfp) fusion (a proxy of the glycerol-3-phosphate [G3P] dehydrogenase activity) linked the macroscopic phenotype to the expression of the glp genes. Either deleting glpR (encoding the G3P-responsive transcriptional repressor that controls the expression of the glpFKRD gene cluster) or altering G3P formation (by overexpressing glpK, encoding glycerol kinase) abolished the bimodal glpD expression. These manipulations eliminated the stochastic growth start by shortening the otherwise long lag phase. Provision of glpR in trans restored the phenotypes lost in the ΔglpR mutant. The prolonged nongrowth regime of P. putida on glycerol could thus be traced to the regulatory device controlling the transcription of the glp genes. Since the physiological agonist of GlpR is G3P, the arrangement of metabolic and regulatory components at this checkpoint merges a positive feedback loop with a nonlinear transcriptional response, a layout fostering the observed time-dependent shift between two alternative physiological states. Phenotypic variation is a widespread attribute of prokaryotes that leads, inter alia, to the emergence of persistent bacteria, i.e., live but nongrowing members within a genetically clonal population. Persistence allows a fraction of cells to avoid the killing caused by conditions or agents that destroy most growing bacteria (e.g., some antibiotics). Known molecular mechanisms underlying the phenomenon include genetic changes, epigenetic variations, and feedback-based multistability. We show that a prolonged nongrowing state of the bacterial population can be brought about by a distinct regulatory architecture of metabolic genes when cells face specific nutrients (e.g., glycerol). Pseudomonas putida may have adopted the resulting carbon source-dependent metabolic bet hedging as an advantageous trait for exploring new chemical and nutritional landscapes. Defeating such naturally occurring adaptive features of environmental bacteria is instrumental in improving the performance of these microorganisms as whole-cell catalysts in a bioreactor setup.
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