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Folia Microbiologica Oct 2021Rhodococcus spp. strains are widespread in diverse natural and anthropized environments thanks to their high metabolic versatility, biodegradation activities, and unique... (Review)
Review
Rhodococcus spp. strains are widespread in diverse natural and anthropized environments thanks to their high metabolic versatility, biodegradation activities, and unique adaptation capacities to several stress conditions such as the presence of toxic compounds and environmental fluctuations. Additionally, the capability of Rhodococcus spp. strains to produce high value-added products has received considerable attention, mostly in relation to lipid accumulation. In relation with this, several works carried out omic studies and genome comparative analyses to investigate the genetic and genomic basis of these anabolic capacities, frequently in association with the bioconversion of renewable resources and low-cost substrates into triacylglycerols. This review is focused on these omic analyses and the genetic and metabolic approaches used to improve the biosynthetic and bioconversion performance of Rhodococcus. In particular, this review summarizes the works that applied heterologous expression of specific genes and adaptive laboratory evolution approaches to manipulate anabolic performance. Furthermore, recent molecular toolkits for targeted genome editing as well as genome-based metabolic models are described here as novel and promising strategies for genome-scaled rational design of Rhodococcus cells for efficient biosynthetic processes application.
Topics: Biodegradation, Environmental; Genome, Bacterial; Genomics; Metabolic Engineering; Rhodococcus; Systems Biology
PubMed: 34215934
DOI: 10.1007/s12223-021-00892-y -
Journal of Microbiology and... Jul 2018The genus is a phylogenetically and catabolically diverse group that has been isolated from diverse environments, including polar and alpine regions, for its versatile... (Review)
Review
The genus is a phylogenetically and catabolically diverse group that has been isolated from diverse environments, including polar and alpine regions, for its versatile ability to degrade a wide variety of natural and synthetic organic compounds. Their metabolic capacity and diversity result from their diverse catabolic genes, which are believed to be obtained through frequent recombination events mediated by large catabolic plasmids. Many rhodococci have been used commercially for the biodegradation of environmental pollutants and for the biocatalytic production of high-value chemicals from low-value materials. Recent studies of their physiology, metabolism, and genome have broadened our knowledge regarding the diverse biotechnological applications that exploit their catabolic enzymes and pathways.
Topics: Biocatalysis; Biodegradation, Environmental; Biotechnology; Cholesterol; Environmental Pollutants; Genome, Bacterial; Industrial Microbiology; Lignin; Metabolic Networks and Pathways; Phylogeny; Plasmids; Rhodococcus; Soil Microbiology; Terpenes; Xylenes
PubMed: 29913546
DOI: 10.4014/jmb.1712.12017 -
Applied and Environmental Microbiology Apr 2022Isoprene (2-methyl-1,3-butadiene) is a climate-active gas released to the atmosphere in large quantities, comparable to methane in magnitude. Several bacteria have been...
Isoprene (2-methyl-1,3-butadiene) is a climate-active gas released to the atmosphere in large quantities, comparable to methane in magnitude. Several bacteria have been isolated which can grow on isoprene as a sole carbon and energy source, but very little information is available about the degradation of isoprene by these bacteria at the biochemical level. Isoprene utilization is dependent on a multistep pathway, with the first step being the oxidation of isoprene to epoxy-isoprene. This is catalyzed by a four-component soluble diiron monooxygenase, isoprene monooxygenase (IsoMO). IsoMO is a six-protein complex comprising an oxygenase (IsoABE), containing the di-iron active site, a Rieske-type ferredoxin (IsoC), a NADH reductase (IsoF), and a coupling/effector protein (IsoD), homologous to the soluble methane monooxygenase and alkene/aromatic monooxygenases. Here, we describe the purification of the IsoMO components from sp. AD45 and reconstitution of isoprene-oxidation activity . Some IsoMO components were expressed and purified from the homologous host sp. AD45-ID, a sp. AD45 strain lacking the megaplasmid which contains the isoprene metabolic gene cluster. Others were expressed in Escherichia coli and purified as fusion proteins. We describe the characterization of these purified components and demonstrate their activity when combined with sp. AD45 cell lysate. Demonstration of IsoMO activity provides a platform for further biochemical and biophysical characterization of this novel soluble diiron center monooxygenase, facilitating new insights into the enzymatic basis for the bacterial degradation of isoprene. Isoprene is a highly abundant climate-active gas and a carbon source for some bacteria. Analyses of the genes encoding isoprene monooxygenase (IsoMO) indicate this enzyme is a soluble diiron center monooxygenase in the same family of oxygenases as soluble methane monooxygenase, alkene monooxygenase, and toluene monooxygenase. We report the initial biochemical characterization of IsoMO from , the first from any bacterium, describing the challenging purification and reconstitution of activity of its four components. This study lays the foundation for future detailed mechanistic studies of IsoMO, a key enzyme in the global isoprene cycle.
Topics: Butadienes; Carbon; Hemiterpenes; Mixed Function Oxygenases; Oxygenases; Rhodococcus
PubMed: 35285709
DOI: 10.1128/aem.00029-22 -
Molecular Microbiology Jul 2019Rhodococcus equi is the only recognized animal pathogenic species within an extended genus of metabolically versatile Actinobacteria of considerable biotechnological... (Review)
Review
Rhodococcus equi is the only recognized animal pathogenic species within an extended genus of metabolically versatile Actinobacteria of considerable biotechnological interest. Best known as a horse pathogen, R. equi is commonly isolated from other animal species, particularly pigs and ruminants, and causes severe opportunistic infections in people. As typical in the rhodococci, R. equi niche specialization is extrachromosomally determined, via a conjugative virulence plasmid that promotes intramacrophage survival. Progress in the molecular understanding of R. equi and its recent rise as a novel paradigm of multihost adaptation has been accompanied by an unusual nomenclatural instability, with a confusing succession of names: "Prescottia equi", "Prescotella equi", Corynebacterium hoagii and Rhodococcus hoagii. This article reviews current advances in the genomics, biology and virulence of this pathogenic actinobacterium with a unique mechanism of plasmid-transferable animal host tropism. It also discusses the taxonomic and nomenclatural issues around R. equi in the light of recent phylogenomic evidence that confirms its membership as a bona fide Rhodococcus.
Topics: Actinomycetales Infections; Animals; Genomics; Horses; Phylogeny; Plasmids; Rhodococcus; Rhodococcus equi; Swine; Virulence
PubMed: 31099908
DOI: 10.1111/mmi.14267 -
Genes May 2019Tetralin (1,2,3,4-tetrahydonaphthalene) is a recalcitrant compound that consists of an aromatic and an alicyclic ring. It is found in crude oils, produced industrially... (Review)
Review
Tetralin (1,2,3,4-tetrahydonaphthalene) is a recalcitrant compound that consists of an aromatic and an alicyclic ring. It is found in crude oils, produced industrially from naphthalene or anthracene, and widely used as an organic solvent. Its toxicity is due to the alteration of biological membranes by its hydrophobic character and to the formation of toxic hydroperoxides. Two unrelated bacteria, strain TFA and sp. strain TFB were isolated from the same niche as able to grow on tetralin as the sole source of carbon and energy. In this review, we provide an overview of current knowledge on tetralin catabolism at biochemical, genetic and regulatory levels in both strains. Although they share the same biodegradation strategy and enzymatic activities, no evidences of horizontal gene transfer between both bacteria have been found. Moreover, the regulatory elements that control the expression of the gene clusters are completely different in each strain. A special consideration is given to the complex regulation discovered in TFA since three regulatory systems, one of them involving an unprecedented communication between the catabolic pathway and the regulatory elements, act together at transcriptional and posttranscriptional levels to optimize tetralin biodegradation gene expression to the environmental conditions.
Topics: Biodegradation, Environmental; Genomics; Humans; Petroleum; Rhodococcus; Sphingomonadaceae; Tetrahydronaphthalenes
PubMed: 31064110
DOI: 10.3390/genes10050339 -
Molecules (Basel, Switzerland) Aug 2021Bacteria belonging to the genus are frequent components of microbial communities in diverse natural environments. Some rhodococcal species exhibit the outstanding... (Review)
Review
Bacteria belonging to the genus are frequent components of microbial communities in diverse natural environments. Some rhodococcal species exhibit the outstanding ability to produce significant amounts of triacylglycerols (TAG) (>20% of cellular dry weight) in the presence of an excess of the carbon source and limitation of the nitrogen source. For this reason, they can be considered as oleaginous microorganisms. As occurs as well in eukaryotic single-cell oil (SCO) producers, these bacteria possess specific physiological properties and molecular mechanisms that differentiate them from other microorganisms unable to synthesize TAG. In this review, we summarized several of the well-characterized molecular mechanisms that enable oleaginous rhodococci to produce significant amounts of SCO. Furthermore, we highlighted the ability of these microorganisms to degrade a wide range of carbon sources coupled to lipogenesis. The qualitative and quantitative oil production by rhodococci from diverse industrial wastes has also been included. Finally, we summarized the genetic and metabolic approaches applied to oleaginous rhodococci to improve SCO production. This review provides a comprehensive and integrating vision on the potential of oleaginous rhodococci to be considered as microbial biofactories for microbial oil production.
Topics: Biofuels; Carbon; Lipogenesis; Oils; Phylogeny; Rhodococcus
PubMed: 34443455
DOI: 10.3390/molecules26164871 -
ELife Dec 2017The acquisition of a virulence plasmid is sufficient to turn a beneficial strain of bacteria into a pathogen.
The acquisition of a virulence plasmid is sufficient to turn a beneficial strain of bacteria into a pathogen.
Topics: Bacterial Proteins; Biological Evolution; Plant Diseases; Plasmids; Rhodococcus; Virulence
PubMed: 29231817
DOI: 10.7554/eLife.33383 -
Chemosphere Mar 20092-Aminobenzothiazole (ABT) degradation was investigated using free and immobilized systems during photodegradation under solar light in the presence of...
2-Aminobenzothiazole (ABT) degradation was investigated using free and immobilized systems during photodegradation under solar light in the presence of Fe(III)-nitrilotriacetic acid (FeNTA), biodegradation by Rhodococcus rhodochrous, and during combined conditions. Ca-alginate hydrogel was chosen as a model matrix and some complementary studies were required to characterize this new system. R. rhodochrous metabolism in this type of environment was monitored by NMR spectroscopy. Neither change in intracellular pH values nor in ATP concentrations was observed by in vivo(31)P NMR, showing that no metabolic modification occurred between free and immobilized cells. (1)H NMR demonstrated that alginate was not used as carbon source by R. rhodochrous. After establishing the pre-treatment protocol by SPE to eliminate solubilised alginate, ABT adsorption on beads and degradation were studied. The same pathways of transformation were observed in suspended and immobilized cell systems. Considering the ABT adsorption phenomenon on alginate beads (8%), the efficiency of the two systems was found to be comparable although the degradation rate was slightly lower with immobilized cells. The most important result was the finding that the positive effect of FeNTA on ABT degradation with immobilized cells was similar to that observed previously with free cells. All these results show that mechanisms observed with free cells can be extrapolated to entrapped cells, i.e. under conditions much closer to those usually encountered in the environment.
Topics: Alginates; Benzothiazoles; Biotransformation; Cells, Immobilized; Chromatography, Liquid; Ferric Compounds; Glucuronic Acid; Hexuronic Acids; Light; Magnetic Resonance Spectroscopy; Nitrilotriacetic Acid; Photolysis; Rhodococcus; Time Factors
PubMed: 19103458
DOI: 10.1016/j.chemosphere.2008.11.021 -
Scientific Reports Dec 2022Adhesive activities of hydrocarbon-oxidizing Rhodococcus bacteria towards solid hydrocarbons, effects of adhesion on biodegradation of these compounds by rhodococcal...
Adhesive activities of hydrocarbon-oxidizing Rhodococcus bacteria towards solid hydrocarbons, effects of adhesion on biodegradation of these compounds by rhodococcal cells and adhesion mechanisms of Rhodococcus spp. were studied in this work. It was shown that efficiency of Rhodococcus cells' adhesion to solid n-alkanes and polycyclic aromatic hydrocarbons (PAHs) varied from 0.0 to 10.6·10 CFU/cm. R. erythropolis IEGM 212 and R. opacus IEGM 262 demonstrated the highest (≥ 4.3·10 CFU/cm) adhesion. The percentage biodegradation of solid hydrocarbons (n-hexacosane and anthracene as model substrates) by Rhodococcus cells was 5 to 60% at a hydrocarbon concentration of 0.2% (w/w) after 9 days and strongly depended on cell adhesive activities towards these compounds (r ≥ 0.71, p < 0.05). No strict correlation between the adhesive activities of rhodococcal cells and physicochemical properties of bacteria and hydrocarbons was detected. Roughness of the cell surface was a definitive factor of Rhodococcus cell adhesion to solid hydrocarbons. Specific appendages with high adhesion force (≥ 0.6 nN) and elastic modulus (≥ 6 MPa) were found on the surface of Rhodococcus cells with high surface roughness. We hypothesized that these appendages participated in the adhesion process.
Topics: Rhodococcus; Hydrocarbons; Biodegradation, Environmental; Alkanes; Polycyclic Aromatic Hydrocarbons
PubMed: 36513758
DOI: 10.1038/s41598-022-26173-3 -
International Journal of Molecular... Sep 2019The application of purified enzymes as well as whole-cell biocatalysts in synthetic organic chemistry is becoming more and more popular, and both academia and industry... (Review)
Review
The application of purified enzymes as well as whole-cell biocatalysts in synthetic organic chemistry is becoming more and more popular, and both academia and industry are keen on finding and developing novel enzymes capable of performing otherwise impossible or challenging reactions. The diverse genus offers a multitude of promising enzymes, which therefore makes it one of the key bacterial hosts in many areas of research. This review focused on the broad utilization potential of the genus in organic chemistry, thereby particularly highlighting the specific enzyme classes exploited and the reactions they catalyze. Additionally, close attention was paid to the substrate scope that each enzyme class covers. Overall, a comprehensive overview of the applicability of the genus is provided, which puts this versatile microorganism in the spotlight of further research.
Topics: Biocatalysis; Catalysis; Chemistry Techniques, Synthetic; Hydrolases; Metabolic Networks and Pathways; Nitriles; Oxidation-Reduction; Oximes; Rhodococcus; Sulfur Compounds
PubMed: 31561555
DOI: 10.3390/ijms20194787