KT2440: the long journey of a soil-dweller to become a synthetic biology chassis.

Although members of the genus share specific morphological, metabolic, and genomic traits, the diversity of niches and lifestyles adopted by the family members is vast. One species of the group, thrives as a colonizer of plant roots and frequently inhabits soils polluted with various types of chemical waste. Owing to a combination of historical contingencies and inherent qualities, a particular strain, KT2440, emerged time ago as an archetype of an environmental microorganism amenable to recombinant DNA technologies, which was also capable of catabolizing chemical pollutants.

Draft genome sequence of three hydrocarbon-degrading strains isolated from an abandoned century-old oil exploration well.

We present genome sequences of three strains isolated from an abandoned century-old oil exploration well. A sp. genome showed a size of 5,378,420 bp, while genomes sized 3,522,593 and 3,864,311 bp.

Comparative genomics of (): diversity, habitats, and biodegradation of aromatic compounds.

() has been found principally in oil-polluted environments. The capability of to thrive from the degradation of pollutant compounds makes it a species of interest for potential bioremediation applications. However, little has been reported about the diversity of .

Identification of a Phylogenetically Divergent Vanillate O-Demethylase from R1 Supporting Growth on -Methoxylated Aromatic Acids.

Rieske-type two-component vanillate O-demethylases (VanODs) catalyze conversion of the lignin-derived monomer vanillate into protocatechuate in several bacterial species. Currently, VanODs have received attention because of the demand of effective lignin valorization technologies, since these enzymes own the potential to catalyze methoxy group demethylation of distinct lignin monomers. In this work, we identified a phylogenetically divergent VanOD from R1, only distantly related to previously described homologues and whose presence, along with a 3-hydroxybenzoate/gentisate pathway, correlated with the ability to grow on other meta-methoxylated aromatics, such as 3-methoxybenzoate and 5-methoxysalicylate.

Genome-Wide Metabolic Reconstruction of the Synthesis of Polyhydroxyalkanoates from Sugars and Fatty Acids by Sensu Lato Species.

sensu lato (s.l.) species have a versatile metabolism.

Identification of a self-sufficient cytochrome P450 monooxygenase from Cupriavidus pinatubonensis JMP134 involved in 2-hydroxyphenylacetic acid catabolism, via homogentisate pathway.

The self-sufficient cytochrome P450 RhF and its homologues belonging to the CYP116B subfamily have attracted considerable attention due to the potential for biotechnological applications based in their ability to catalyse an array of challenging oxidative reactions without requiring additional protein partners. In this work, we showed for the first time that a CYP116B self-sufficient cytochrome P450 encoded by the ohpA gene harboured by Cupriavidus pinatubonensis JMP134, a β-proteobacterium model for biodegradative pathways, catalyses the conversion of 2-hydroxyphenylacetic acid (2-HPA) into homogentisate. Mutational analysis and HPLC metabolite detection in strain JMP134 showed that 2-HPA is degraded through the well-known homogentisate pathway requiring a 2-HPA 5-hydroxylase activity provided by OhpA, which was additionally supported by heterologous expression and enzyme assays.

Widespread distribution of genes in Proteobacteria reveals key enzymes for 5-hydroxymethylfurfural conversion.

Furans represent a class of promising chemicals, since they constitute valuable intermediates in conversion of biomass into sustainable products intended to replace petroleum-derivatives. Conversely, generation of furfural and 5-hydroxymethylfurfural (HMF) as by-products in lignocellulosic hydrolysates is undesirable due its inhibitory effect over fermentative microorganisms. Therefore, the search for furans-metabolizing bacteria has gained increasing attention since they are valuable tools to solve these challenging issues.

Complete Multipartite Genome Sequence of the Cupriavidus basilensis Type Strain, a 2,6-Dichlorophenol-Degrading Bacterium.

We report the complete 8.94-Mb genome sequence of the type strain of (DSM 11853 = CCUG 49340 = RK1), formed by two chromosomes and six putative plasmids, which offers insights into its chloroaromatic-biodegrading capabilities.

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.

Novel Genes Involved in Resistance to Both Ultraviolet Radiation and Perchlorate From the Metagenomes of Hypersaline Environments.

Microorganisms that thrive in hypersaline environments on the surface of our planet are exposed to the harmful effects of ultraviolet radiation. Therefore, for their protection, they have sunscreen pigments and highly efficient DNA repair and protection systems. The present study aimed to identify new genes involved in UV radiation resistance from these microorganisms, many of which cannot be cultured in the laboratory.

Draft Genome Sequences of Two Strains That Are Able To Use Furan Derivatives as Their Sole Carbon Source.

sp. strains ALS1279 and ALS1131 were isolated from wastewater treatment facilities on the basis of their ability to use furfural, a key lignocellulose-derived inhibitor, as their only carbon source. Here, we present the draft genome sequences of both strains, which can shed light on catabolic pathways for furan compounds in pseudomonads.

Complete Genome Sequence of Rhodococcus ruber R1, a Novel Strain Showing a Broad Catabolic Potential toward Lignin-Derived Aromatics.

R1 was isolated from a pulp mill wastewater treatment plant because of its ability to use methoxylated aromatics as growth substrates. We report the 5.56-Mb genome sequence of strain R1, which can provide insights into the biodegradation of lignin-derived phenolic monomers and potentially support processes for lignocellulose conversion.

Evolving metabolism of 2,4-dinitrotoluene triggers SOS-independent diversification of host cells.

The molecular mechanisms behind the mutagenic effect of reactive oxygen species (ROS) released by defective metabolization of xenobiotic 2,4-dinitrotoluene (DNT) by a still-evolving degradation pathway were studied. To this end, the genes required for biodegradation of DNT from Burkholderia cepacia R34 were implanted in Escherichia coli and the effect of catabolizing the nitroaromatic compound monitored with stress-related markers and reporters. Such a proxy of the naturally-occurring scenario faithfully recreated the known accumulation of ROS caused by faulty metabolism of DNT and the ensuing onset of an intense mutagenesis regime.

Draft genome sequences of strains CS-508 and MVCC14, isolated from freshwater bloom events in Australia and Uruguay.

Members of the genus represent an important environmental and health concern. Strains CS-508 and MVCC14 of were isolated from freshwater reservoirs located in Australia and Uruguay, respectively. While CS-508 has been reported as non-toxic, MVCC14 is a saxitoxin (STX) producer.

Diurnal Changes in Active Carbon and Nitrogen Pathways Along the Temperature Gradient in Porcelana Hot Spring Microbial Mat.

Composition, carbon and nitrogen uptake, and gene transcription of microbial mat communities in Porcelana neutral hot spring (Northern Chilean Patagonia) were analyzed using metagenomics, metatranscriptomics and isotopically labeled carbon (HCO) and nitrogen (NHCl and KNO) assimilation rates. The microbial mat community included 31 phyla, of which only and were dominant. At 58°C both phyla co-occurred, with similar contributions in relative abundances in metagenomes and total transcriptional activity.

The interplay of EIIA with C-source regulation of the Pu promoter of Pseudomonas putida mt-2.

The presence of some sugars (e.g. glucose) downregulates the activity of the Pu promoter of plasmid pWW0 of Pseudomonas putida mt-2, which drives the upper TOL operon for biodegradation of m-xylene.

The Metabolic Redox Regime of Pseudomonas putida Tunes Its Evolvability toward Novel Xenobiotic Substrates.

During evolution of biodegradation pathways for xenobiotic compounds involving Rieske nonheme iron oxygenases, the transition toward novel substrates is frequently associated with faulty reactions. Such events release reactive oxygen species (ROS), which are endowed with high mutagenic potential. In this study, we evaluated how the operation of the background metabolic network by an environmental bacterium may either foster or curtail the still-evolving pathway for 2,4-dinitrotoluene (2,4-DNT) catabolism.

Genomic features of "Candidatus Venteria ishoeyi", a new sulfur-oxidizing macrobacterium from the Humboldt Sulfuretum off Chile.

The Humboldt Sulfuretum (HS), in the productive Humboldt Eastern Boundary Current Upwelling Ecosystem, extends under the hypoxic waters of the Peru-Chile Undercurrent (ca. 6°S and ca. 36°S).

Cupriavidus pinatubonensis AEO106 deals with copper-induced oxidative stress before engaging in biodegradation of the herbicide 4-chloro-2-methylphenoxyacetic acid.

Background: Microbial degradation of phenoxy acid (PA) herbicides in agricultural soils is important to minimize herbicide leaching to groundwater reservoirs. Degradation may, however, be hampered by exposure of the degrader bacteria to toxic metals as copper (Cu) in the soil environment. Exposure to Cu leads to accumulation of intracellular reactive oxygen species (ROS) in some bacteria, but it is not known how Cu-derived ROS and an ensuing oxidative stress affect the degradation of PA herbicides.

Plasmid and clonal interference during post horizontal gene transfer evolution.

Plasmids are nucleic acid molecules that can drive their own replication in a living cell. They can be transmitted horizontally and can thrive in the host cell to high-copy numbers. Plasmid replication and gene expression consume cellular resources and cells carrying plasmids incur fitness costs.

Pyridine nucleotide transhydrogenases enable redox balance of Pseudomonas putida during biodegradation of aromatic compounds.

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.

Pseudomonas putida mt-2 tolerates reactive oxygen species generated during matric stress by inducing a major oxidative defense response.

Background: Soil bacteria typically thrive in water-limited habitats that cause an inherent matric stress to the cognate cells. Matric stress gives rise to accumulation of intracellular reactive oxygen species (ROS), which in turn may induce oxidative stress, and even promote mutagenesis. However, little is known about the impact of ROS induced by water limitation on bacteria performing important processes as pollutant biodegradation in the environment.

High-resolution analysis of the m-xylene/toluene biodegradation subtranscriptome of Pseudomonas putida mt-2.

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.