32 research outputs found
Regulation of PTS systems and their interplay with central carbon metabolism in Pseudomonas putida
Tesis doctoral inédita. Universidad Autónoma de Madrid, Facultad de Ciencias, Departamento de Biología Molecular. Fecha de lectura: 29-06-201
The Bacterial Product Violacein Exerts an Immunostimulatory Effect Via TLR8
Violacein, an indole-derived, purple-colored natural pigment isolated from Chromobacterium violaceum has shown multiple biological activities. In this work, we studied the effect of violacein in different immune cell lines, namely THP-1, MonoMac 6, ANA-1, Raw 264.7 cells, as well as in human peripheral blood mononuclear cells (PBMCs). A stimulation of TNF-α production was observed in murine macrophages (ANA-1 and Raw 264.7), and in PBMCs, IL-6 and IL-1β secretion was detected. We obtained evidence of the molecular mechanism of activation by determining the mRNA expression pattern upon treatment with violacein in Raw 264.7 cells. Incubation with violacein caused activation of pathways related with an immune and inflammatory response. Our data utilizing TLR-transfected HEK-293 cells indicate that violacein activates the human TLR8 (hTLR8) receptor signaling pathway and not human TLR7 (hTLR7). Furthermore, we found that the immunostimulatory effect of violacein in PBMCs could be suppressed by the specific hTLR8 antagonist, CU-CPT9a. Finally, we studied the interaction of hTLR8 with violacein in silico and obtained evidence that violacein could bind to hTLR8 in a similar fashion to imidazoquinoline compounds. Therefore, our results indicate that violacein may have some potential in contributing to future immune therapy strategies.Universidad de Costa Rica/[801-B2-519]/UCR/Costa RicaMinisterio de Ciencia, Tecnología y Telecomunicaciones/[FI-497-11]/MICITT/Costa RicaMinisterio de Ciencia, Tecnología y Telecomunicaciones/[DFG-TR84]/MICITT/Costa RicaMinisterio de Ciencia, Tecnología y Telecomunicaciones/[DFG-KFO325]/MICITT/Costa RicaUCR::Vicerrectoría de Docencia::Ciencias Básicas::Facultad de Ciencias::Escuela de QuímicaUCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias Básicas::Centro de Investigaciones en Productos Naturales (CIPRONA)UCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias Básicas::Centro de Investigación en Biología Celular y Molecular (CIBCM)UCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias de la Salud::Instituto de Investigaciones Farmacéuticas (INIFAR
Special Issue: Diversity of Extremophiles in Time and Space
Extreme environments are fascinating ecosystems that have allowed us to increase
our knowledge about the evolutionary processes of life [1], develop new biotechnological
applications (e.g., industrial applications of lipases [2], and thermostable DNA Polymerases
in PCR tests [3]) and establish some fundamental concepts about the origins of life and
the search for life in the Universe [1]. Despite the fact that research on the living beings
that inhabit these extreme environments (i.e., extremophiles) began more than five decades
ago with the pioneering works of Thomas D. Brock [4], nowadays, we still have a lot to
learn about microbial diversity, and especially about the metabolism and biochemistry
of these microorganisms; therefore, the study of extremophiles, extremozymes and their
biotechnological potential remains a hot topic.Universidad de Costa Rica/[809-B6-524]/UCR/Costa RicaEuropean Union’s Horizon/[892961]/EU/Unión EuropeaUCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias Básicas::Centro de Investigaciones en Productos Naturales (CIPRONA
Quantitative Physiology Approaches to Understand and Optimize Reducing Power Availability in Environmental Bacteria
The understanding of how carbon fluxes are distributed through a metabolic network offers an overview of the pathways that a given microorganism uses to produce energy, reducing power, and biomass. These invaluable data are related to the physiological state of the cell and provide information about the metabolic potential of microorganisms for specific environmental and biotechnological applications such as the degradation of toxic compounds (e.g., hydrocarbons) or the targeted production of high value-added products (e.g., lipids). Here, we propose a general approach to explore the pathways involved in NADPH balance in bacteria, which are in turn responsible for maintaining redox homeostasis and endowing the microorganism with the ability to counteract oxidative stress. We focus on the fluxes catalyzed by NADP+-dependent enzymes in the metabolic network of the model soil bacterium Pseudomonas putida KT2440. This environmental microorganism is a promising cell factory for a number of NADPH-dependent biotransformations, including industrial and bioremediation processes. The relevant enzymes involved in redox balance in strain KT2440 are (1) glucose-6-phosphate dehydrogenase, (2) 6-phosphogluconate dehydrogenase, (3) isocitrate dehydrogenase, (4) malic enzyme, and (5) 2-keto-6-phosphogluconate reductase. NADPH can be generated or consumed by other enzymatic reactions depending on the microorganism; however, the first four enzymes listed above are recognized as a major source of reducing power in a wide variety of microorganisms. The present protocol includes a first stage in which the NADPH balance is derived from fluxomic data and in vitro enzymatic assays. A second step is then proposed, where the redox ratios of pyridine dinucleotides and the cell capacity to counter oxidative stress are qualitatively correlated.UCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias Básicas::Centro de Investigaciones en Productos Naturales (CIPRONA)UCR::Vicerrectoría de Docencia::Ciencias Básicas::Facultad de Ciencias::Escuela de Químic
The potential of Pseudomonas for bioremediation of oxyanions
Non-metal, metal and metalloid oxyanions occur naturally
in minerals and rocks of the Earth’s crust and
are mostly found in low concentrations or confined
in specific regions of the planet. However, anthropogenic
activities including urban development, mining,
agriculture, industrial activities and new technologies
have increased the release of oxyanions to the environment,
which threatens the sustainability of natural
ecosystems, in turn affecting human development.
For these reasons, the implementation of new
methods that could allow not only the remediation of
oxyanion contaminants but also the recovery of valuable
elements from oxyanions of the environment is
imperative. From this perspective, the use of microorganisms
emerges as a strategy complementary to
physical, mechanical and chemical methods. In this
review, we discuss the opportunities that the Pseudomonas
genus offers for the bioremediation of
oxyanions, which is derived from its specialized central
metabolism and the high number of oxidoreductases
present in the genomes of these bacteria.
Finally, we review the current knowledge on the
transport and metabolism of specific oxyanions in
Pseudomonas species. We consider that the
Pseudomonas genus is an excellent starting point for
the development of biotechnological approaches for
the upcycling of oxyanions into added-value metal
and metalloid byproducts.UCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias Básicas::Centro de Investigaciones en Productos Naturales (CIPRONA)UCR::Vicerrectoría de Docencia::Ciencias Básicas::Facultad de Ciencias::Escuela de Químic
Concomitant prediction of environmental fate and toxicity of chemical compounds
The environmental fate of many functional molecules that are produced on a large scale as precursors or as additives to specialty goods (plastics, fibers, construction materials, etc.), let alone those synthesized by the pharmaceutical industry, is generally unknown. Assessing their environmental fate is crucial when taking decisions on the manufacturing, handling, usage, and release of these substances, as is the evaluation of their toxicity in humans and other higher organisms. While this data are often hard to come by, the experimental data already available on the biodegradability and toxicity of many unusual compounds (including genuinely xenobiotic molecules) make it possible to develop machine learning systems to predict these features. As such, we have created a predictor of the “risk” associated with the use and release of any chemical. This new system merges computational methods to predict biodegradability with others that assess biological toxicity. The combined platform, named BiodegPred (https://sysbiol.cnb.csic.es/BiodegPred/), provides an informed prognosis of the chance a given molecule can eventually be catabolized in the biosphere, as well as of its eventual toxicity, all available through a simple web interface. While the platform described does not give much information about specific degradation kinetics or particular biodegradation pathways, BiodegPred has been instrumental in anticipating the probable behavior of a large number of new molecules (e.g. antiviral compounds) for which no biodegradation data previously existed.UCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias Básicas::Centro de Investigaciones en Productos Naturales (CIPRONA
Transcriptional control of 2,4-dinitrotoluene degradation in Burkholderia sp. R34 bears a regulatory patch that eases pathway evolution
The dnt pathway of Burkholderia sp. R34 is in the
midst of an evolutionary journey from its ancestral,
natural substrate (naphthalene) towards a new xenobiotic
one [2,4-dinitrotoluene (DNT)]. The gene cluster
encoding the leading multicomponent ring
dioxygenase (DntA) has activity on the old and the
new substrate, but it is induced by neither. Instead, the
transcriptional factor encoded by the adjacent gene
(dntR) activates expression of the dnt cluster upon
addition of salicylate, one degradation intermediate of
the ancestral naphthalene route but not any longer a
substrate/product of the evolved DntA enzyme. Fluorescence
of cells bearing dntA-gfp fusions revealed
that induction of the dnt genes by salicylate was
enhanced upon exposure to bona fide DntA substrates,
i.e., naphthalene or DNT. Such amplification
was dependent on effective dioxygenation of these
pathway-specific head compounds, which thereby fostered
expression of the cognate catabolic operon. The
phenomenon seems to happen not through direct
binding to a cognate transcriptional factor but through
the interplay of a non-specific regulator with a
substrate-specific enzyme. This regulatory scenario
may ease transition of complete catabolic operons
(i.e. enzymes plus regulatory devices) from one substrate
to another without loss of fitness during the evolutionary
roadmap between two optimal specificities.Sociedad Española de Trombosis y Hemostasia/[RTI2018-095584-B-C42]/SETH/EspañaSynthetic microbial communities for the production of limonene derived products/[ERA-COBIOTECH 2018 - PCI2019- 111859-2]/SyCoLiM/Reino UnidoMadonna University/[H2020-FET-OPEN-RIA-2017-1-766975]/MADONNA/Estados UnidosBioRoboost/[H2020-NMBP-BIO-CSA-2018-820699]//Unión EuropeaSynBio4Flav/[H2020-NMBP-TR-IND/H2020-NMBP-BIO-2018- 814650]//Unión EuropeaIngeniería Microbiana, Salud y Calidad de Vida/[S2017/BMD-3691]/InGEMICS-CM/EspañaMIX-UP/[MIX-UP H2020-BIO-CN-2019-870294]//Unión EuropeaUCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias Básicas::Centro de Investigaciones en Productos Naturales (CIPRONA
ArsH protects Pseudomonas putida from oxidative damage caused by exposure to arsenic
The two As resistance arsRBC operons of Pseudomonas putida KT2440 are followed by a downstream gene called arsH that encodes an NADPH‐dependent flavin mononucleotide reductase. In this work, we show that the arsH1 and (to a lesser extent) arsH2 genes of P. putida KT2440 strengthened its tolerance to both inorganic As(V) and As(III) and relieved the oxidative stress undergone by cells exposed to either oxyanion. Furthermore, overexpression of arsH1 and arsH2 endowed P. putida with a high tolerance to the oxidative stress caused by diamide (a drainer of metabolic NADPH) in the absence of any arsenic. To examine whether the activity of ArsH was linked to a direct action on the arsenic compounds tested, arsH1 and arsH2 genes were expressed in Escherichia coli, which has an endogenous arsRBC operon but lacks an arsH ortholog. The resulting clones both deployed a lower production of reactive oxygen species (ROS) when exposed to As salts and had a superior endurance to physiological redox insults. These results suggest that besides the claimed direct action on organoarsenicals, ArsH contributes to relieve toxicity of As species by mediating reduction of ROS produced in vivo upon exposure to the oxyanion, e.g. by generating FMNH2 to fuel ROS‐quenching activities.UCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias Básicas::Centro de Investigaciones en Productos Naturales (CIPRONA)UCR::Vicerrectoría de Docencia::Ciencias Básicas::Facultad de Ciencias::Escuela de Químic
Microbial degradation of palm (Elaeis guineensis) biodiesel
La cinética de la biodegradación de los ésteres metílicos y etílicos derivados de palma (biodiesel) por una población silvestre de bacterias aeróbicas fue medida a 20°C, como medición manométrica del consumo de oxígeno. Los ésteres metílicos y etílicos se obtuvieron por transesterificación del aceite de palma con metanol y etanol, respectivamente. La flora bacteriana incluyó a los géneros Bacillus, Proteus, Pseudomonas, Citrobacter y Enterobacter. Las velocidades de consumo de oxígeno para las muestras de biodiesel fueron similares a lo observado en la biodegradación de disoluciones 1.0 mM de sustratos sencillos solubles en agua, tales como carbohidratos, aminoácidos y albúmina de huevo
Scattering of light by colloidal aluminosilicate particles produces the unusual sky-blue color of Río Celeste (Tenorio volcano complex, Costa Rica).
Río Celeste (Sky-Blue River) in Tenorio National Park (Costa Rica), a river that derives from the confluence and mixing of two colorless streams--Río Buenavista (Buenavista River) and Quebrada Agria (Sour Creek)--is renowned in Costa Rica because it presents an atypical intense sky-blue color. Although various explanations have been proposed for this unusual hue of Río Celeste, no exhaustive tests have been undertaken; the reasons hence remain unclear. To understand this color phenomenon, we examined the physico-chemical properties of Río Celeste and of the two streams from which it is derived. Chemical analysis of those streams with ion-exchange chromatography (IC) and inductively coupled plasma atomic emission spectroscopy (ICP-OES) made us discard the hypothesis that the origin of the hue is due to colored chemical species. Our tests revealed that the origin of this coloration phenomenon is physical, due to suspended aluminosilicate particles (with diameters distributed around 566 nm according to a lognormal distribution) that produce Mie scattering. The color originates after mixing of two colorless streams because of the enlargement (by aggregation) of suspended aluminosilicate particles in the Río Buenavista stream due to a decrease of pH on mixing with the acidic Quebrada Agria. We postulate a chemical mechanism for this process, supported by experimental evidence of dynamic light scattering (DLS), zeta potential measurements, X-ray diffraction and scanning electron microscopy (SEM) with energy-dispersive spectra (EDS). Theoretical modeling of the Mie scattering yielded a strong coincidence between the observed color and the simulated one