Rhodococcus Species, Their Resistance to Stress and Biotechnological Potential

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Microbial Biotechnology".

Deadline for manuscript submissions: closed (31 December 2022) | Viewed by 12854

Special Issue Editors


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Guest Editor
Institute of Microbiology of the Academy of Sciences of the Czech Republic, Prague, Czech Republic
Interests: the studies of gene expression control and enzyme systems in laboratory strains of model bacterial species (Escherichia coli) and on construction and analysis of strains of industrial bacteria that are used in biotechnology-based syntheses of various compounds and environmental applications (e.g., Corynebacterium glutamicum, Rhodococcus erythropolis)
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iBB – Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
Interests: bacterial adaptation; marine biotechnology; biocatalysis; bioreactors; bioprocess engineering
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Molecular and Applied Microbiology Lab, Department of Pharmacy and Biotechnology, University of Bologna, Via Irnerio 42, 40126 Bologna, Italy
Interests: bacterial degradation of contaminants; mechanisms of bacterial adaptation to toxic compounds; waste bioconversion into valuable compounds; metal-based nanoparticles; bacterial resistance/tolerance to metals; biodiversity in extreme environments and bioreactors; cave microbiology; bacterial genomics; anti-microbial strategies; biofilms; drug discovery from environmental bacterial isolates
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INBIOP (Institute of Bioscience of Patagonia), National Council of Scientific and Technical Research (CONICET), Faculty of Natural Science and Health Science, University of Patagonia San Juan Bosco, Ruta Provincial N° 1, Km 4-Ciudad Universitaria, Comodoro Rivadavia 9000, Chubut, Argentina
Interests: the physiological and molecular basis of the lipogenesis and oleagenicity in rhodococci, as well as to develop robust strains and processes to the conversion of industrial wastes into precursor oils for biofuels, biolubricants and oleochemicals

Special Issue Information

Dear Colleagues,

The genus Rhodococcus is formed by a group of diverse bacteria, which show great promise for biotechnological applications such as biodegradation, biotransformation, bioremediation, and biosynthesis. These strains are capable of degrading various organic compounds, such as aliphatic and aromatic hydrocarbons, as well as oxygenated and halogenated compounds, including polychlorinated biphenyls, nitroaromatics, heterocyclic compounds, nitriles, and various herbicides. Their ability to resist antibiotics and toxic metal(loid)s (e.g., chromium, tellurium, and arsenic) may be the basis for their use in detoxification processes. Various Rhodococcus species are known to produce acrylamide, triacylglycerols (TAGs), polyhydroxyalkanoates (PHAs), biosurfactants, and carotenoids. Many rhodococci are extremophiles, being able to survive and thrive under hostile conditions, where they can be used for the bioremediation of toxic pollutants. Studies of cell response to diverse types of stress (oxidative, osmotic, heat, and cold) may therefore provide essential knowledge regarding the use of rhodococci in adverse conditions. In addition, some species of this genus are able to thrive under oligotrophic conditions. Several recent studies have described novel genetic engineering methods and advanced genome editing technologies able to manipulate Rhodococcus species for strain improvement and synthetic biology strategies. The aim of this Special Issue is to offer a wide view of the up-to-date knowledge and current trends relating to the biotechnology potential of Rhodococcus.

The editors of this Special Issue of Microorganisms invite you to submit manuscripts concerning any aspect of the biotechnology and stress response of relevant Rhodococcus species.

Dr. Miroslav Pátek
Dr. Carla C. C. R. de Carvalho
Dr. Martina Cappelletti
Prof. Dr. Héctor M. Alvarez
Guest Editors

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Keywords

  • rhodococcus
  • biodegradation
  • biocatalysis
  • biotechnological applications
  • stress response
  • biosynthesis
  • bioconversion
  • omics
  • genetic engineering

Published Papers (5 papers)

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Research

12 pages, 1157 KiB  
Article
Development of Efficient Genome-Reduction Tool Based on Cre/loxP System in Rhodococcus erythropolis
by Wataru Kitagawa and Miyako Hata
Microorganisms 2023, 11(2), 268; https://doi.org/10.3390/microorganisms11020268 - 19 Jan 2023
Cited by 4 | Viewed by 1857
Abstract
Rhodococcus has been extensively studied for its excellent ability to degrade artificial chemicals and its capability to synthesize biosurfactants and antibiotics. In recent years, studies have attempted to use Rhodococcus as a gene expression host. Various genetic tools, such as plasmid vectors, transposon [...] Read more.
Rhodococcus has been extensively studied for its excellent ability to degrade artificial chemicals and its capability to synthesize biosurfactants and antibiotics. In recent years, studies have attempted to use Rhodococcus as a gene expression host. Various genetic tools, such as plasmid vectors, transposon mutagenesis, and gene disruption methods have been developed for use in Rhodococcus; however, no effective method has been reported for performing large-size genome reduction. Therefore, the present study developed an effective plasmid-curing method using the levansucrase-encoding sacB gene and a simple two-step genome-reduction method using a modified Cre/loxP system. For the results, R. erythropolis JCM 2895 was used as the model; a mutant strain that cured all four plasmids and deleted seven chromosomal regions was successfully obtained in this study. The total DNA deletion size was >600 kb, which corresponds mostly to 10% of the genome size. Using this method, a genome-structure-stabilized and unfavorable gene/function-lacking host strain can be created in Rhodococcus. This genetic tool will help develop and improve Rhodococcus strains for various industrial and environmental applications. Full article
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14 pages, 5630 KiB  
Article
Identification of a Phylogenetically Divergent Vanillate O-Demethylase from Rhodococcus ruber R1 Supporting Growth on Meta-Methoxylated Aromatic Acids
by Raúl A. Donoso, Ricardo Corbinaud, Carla Gárate-Castro, Sandra Galaz and Danilo Pérez-Pantoja
Microorganisms 2023, 11(1), 78; https://doi.org/10.3390/microorganisms11010078 - 27 Dec 2022
Viewed by 2338
Abstract
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 [...] Read more.
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 Rhodococcus ruber 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. The complementation of catabolic abilities by heterologous expression in a host strain unable to grow on vanillate, and subsequent resting cell assays, suggest that the vanAB genes of R1 strain encode a proficient VanOD acting on different vanillate-like substrates; and also revealed that a methoxy group in the meta position and a carboxylic acid moiety in the aromatic ring are key for substrate recognition. Phylogenetic analysis of the oxygenase subunit of bacterial VanODs revealed three divergent groups constituted by homologues found in Proteobacteria (Type I), Actinobacteria (Type II), or Proteobacteria/Actinobacteria (Type III) in which the R1 VanOD is placed. These results suggest that VanOD from R1 strain, and its type III homologues, expand the range of methoxylated aromatics used as substrates by bacteria. Full article
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21 pages, 10760 KiB  
Article
Genome-Based Exploration of Rhodococcus Species for Plastic-Degrading Genetic Determinants Using Bioinformatic Analysis
by Jessica Zampolli, Alessandro Orro, Daniele Vezzini and Patrizia Di Gennaro
Microorganisms 2022, 10(9), 1846; https://doi.org/10.3390/microorganisms10091846 - 15 Sep 2022
Cited by 13 | Viewed by 2973
Abstract
Plastic polymer waste management is an increasingly prevalent issue. In this paper, Rhodococcus genomes were explored to predict new plastic-degrading enzymes based on recently discovered biodegrading enzymes for diverse plastic polymers. Bioinformatics prediction analyses were conducted using 124 gene products deriving from diverse [...] Read more.
Plastic polymer waste management is an increasingly prevalent issue. In this paper, Rhodococcus genomes were explored to predict new plastic-degrading enzymes based on recently discovered biodegrading enzymes for diverse plastic polymers. Bioinformatics prediction analyses were conducted using 124 gene products deriving from diverse microorganisms retrieved from databases, literature data, omic-approaches, and functional analyses. The whole results showed the plastic-degrading potential of Rhodococcus genus. Among the species with high plastic-degrading potential, R. erythropolis, R. equi, R. opacus, R. qingshengii, R. fascians, and R. rhodochrous appeared to be the most promising for possible plastic removal. A high number of genetic determinants related to polyester biodegradation were obtained from different Rhodococcus species. However, score calculation demonstrated that Rhodococcus species (especially R. pyridinivorans, R. qingshengii, and R. hoagii) likely possess PE-degrading enzymes. The results identified diverse oxidative systems, including multicopper oxidases, alkane monooxygenases, cytochrome P450 hydroxylases, para-nitrobenzylesterase, and carboxylesterase, and they could be promising reference sequences for the biodegradation of plastics with C−C backbone, plastics with heteroatoms in the main chain, and polyesters, respectively. Notably, the results of this study could be further exploited for biotechnological applications in biodegradative processes using diverse Rhodococcus strains and through catalytic reactions. Full article
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7 pages, 1212 KiB  
Communication
Oligotrophic Gene Expression in Rhodococcus erythropolis N9T-4 under Various Nutrient Conditions
by Yuri Ikeda, Mana Kishimoto, Masaki Shintani and Nobuyuki Yoshida
Microorganisms 2022, 10(9), 1725; https://doi.org/10.3390/microorganisms10091725 - 27 Aug 2022
Cited by 5 | Viewed by 1788
Abstract
Rhodococcus erythropolis N9T-4 is a super oligotroph that grows on an inorganic basal medium without any additional carbon and nitrogen sources and requires CO2 for its oligotrophic growth. Previously, we found that two genes, aldA and mnoA, encoding NAD-dependent aliphatic aldehyde dehydrogenase [...] Read more.
Rhodococcus erythropolis N9T-4 is a super oligotroph that grows on an inorganic basal medium without any additional carbon and nitrogen sources and requires CO2 for its oligotrophic growth. Previously, we found that two genes, aldA and mnoA, encoding NAD-dependent aliphatic aldehyde dehydrogenase and N,N′-dimethyl-4-nitrosoaniline-dependent methanol dehydrogenase, respectively, were highly upregulated under oligotrophic conditions. In this study, we constructed reporter plasmids containing an enhanced green fluorescent protein gene under aldA or mnoA promoters (pAldA and pMnoA, respectively). Fluorescence analysis of N9T-4 cells with reporter plasmids revealed that tryptone and yeast extract strongly repressed the expression of oligotrophy-connected genes, whereas the effect of casamino acids was moderate. Furthermore, remarkably high expression of aldA and mnoA was observed when the reporter strains were grown in media containing primary alcohols, particularly ethanol. Malic acid repressed ethanol-induced gene expression, suggesting that C2 metabolism is involved in the oligotrophic growth of N9T-4. The regulation of oligotrophic gene expression elucidated in this study could provide appropriate conditions for the production of useful compounds in an oligotrophic microbial process. Full article
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20 pages, 4445 KiB  
Article
Effects of Light on Growth and Metabolism of Rhodococcus erythropolis
by Selina Engelhart-Straub, Philipp Cavelius, Fabian Hölzl, Martina Haack, Dania Awad, Thomas Brueck and Norbert Mehlmer
Microorganisms 2022, 10(8), 1680; https://doi.org/10.3390/microorganisms10081680 - 20 Aug 2022
Cited by 8 | Viewed by 2419
Abstract
Rhodococcus erythropolis is resilient to various stressors. However, the response of R. erythropolis towards light has not been evaluated. In this study, R. erythropolis was exposed to different wavelengths of light. Compared to non-illuminated controls, carotenoid levels were significantly increased in white (standard [...] Read more.
Rhodococcus erythropolis is resilient to various stressors. However, the response of R. erythropolis towards light has not been evaluated. In this study, R. erythropolis was exposed to different wavelengths of light. Compared to non-illuminated controls, carotenoid levels were significantly increased in white (standard warm white), green (510 nm) and blue light (470 nm) illuminated cultures. Notably, blue light (455, 425 nm) exhibited anti-microbial effects. Interestingly, cellular lipid composition shifted under light stress, increasing odd chain fatty acids (C15:0, C17:1) cultured under white (standard warm white) and green (510 nm) light. When exposed to blue light (470, 455, 425 nm), fatty acid profiles shifted to more saturated fatty acids (C16:1 to C16:0). Time-resolved proteomics analysis revealed several oxidative stress-related proteins to be upregulated under light illumination. Full article
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