Rhodococcus
Encyclopedia
Rhodococcus is a genus of aerobic, nonsporulating, nonmotile Gram-positive
bacteria closely related to Mycobacteria and Corynebacteria. While a few species are pathogenic, most are benign and have been found to thrive in a broad range of environments, including soil, water, and eukaryotic cells. Fully sequenced in October 2006, the genome is known to be 9.7 megabasepairs long and 67% G/C.
Strains of Rhodococcus are applicably important owing to their ability to catabolize a wide range of compounds and produce bioactive steroids, acrylamide
, and acrylic acid
, and their involvement in fossil fuel biodesulfurization. This genetic and catabolic diversity is not only due to the large bacterial chromosome, but also to the presence of three large linear plasmids. Rhodococcus is also an experimentally advantageous system owing to a relatively fast growth rate and simple developmental cycle. However, as it stands now, Rhodococcus is not well characterized.
Another important application of Rhodococcus comes from bioconversion, using biological systems to convert cheap starting material into more valuable compounds. This use of Rhodococcus is borne out of its ability to metabolize harmful environmental pollutants, such as toluene
, naphthalene
, herbicides, and PCBs. Rhodococci typically metabolize aromatic substrates by first oxygenating the aromatic ring to form a diol (two alcohol groups). Then, the ring is cleaved with intra/extradiol mechanisms, opening the ring and exposing the substrate to further metabolism. Since the chemistry here is very stereospecific, the diols are created with predictable chirality. While controlling the chirality of chemical reaction presents a significant challenge for synthetic chemists, biological processes can be used instead to faithfully produce chiral molecules in cases where direct chemical synthesis is infeasible or inefficient. An example of this is the use of Rhodococcus to produce indene
, a precursor to the AIDS
drug Crixivan(TM), a protease inhibitor, and containing two of the five chiral centers needed in the complex.
of organic pollutant
s. Aromatic compounds are among the most recalcitrant of these pollutants, and lessons can be learned from the recent genomic studies of Rhodococcus sp. strain RHA1, one of the largest bacterial genomes completely sequenced to date. These studies have helped expand the understanding of bacterial catabolism
, noncatabolic physiological adaptation to organic compound
s, and the evolution of large bacterial genome
s. A large number of "peripheral aromatic" pathways funnel a range of natural and xenobiotic
compounds into a restricted number of "central aromatic" pathways. Some pathways are more widespread than initially thought. The Box and Paa pathways illustrate the prevalence of nonoxygenolytic ring-cleavage strategies in aerobic aromatic degradation processes. Functional genomic studies have been useful in establishing that even organisms harboring high numbers of homologous enzymes apparently contain few examples of true redundancy. For example, the multiplicity of ring-cleaving dioxygenases in certain rhodococcal isolates may be attributed to the cryptic aromatic catabolism of different terpenoids and steroids. The large gene repertoires of pollutant degraders such as Rhodococcus RHA1 have evolved principally through more ancient processes. Rhodococcus sp. strain Q1, isolated from soil and paper mill sludge, is able to degrade quinoline
, various pyridine
derivatives, catechol, benzoate, and protocatechuic acid.
and R. equi
. The former, a plant pathogen, causes leafy gall disease in both angiosperm and gymnosperm
plants. R. equi is the causitative agent of foal pneumonia (rattles) and mainly infects foals up to three months in age. However, it has a wide host range, sporadically infecting pigs, cattle and (immunocompromised) humans, in particular AIDS patients and those undergoing immunosuppressive therapy. Interestingly, both pathogens rely on a conjugative virulence plasmid to cause disease. In case of R. fascians, this is a linear plasmid, whereas R. equi harbors a circular plasmid. Both pathogens are economically significant. R. fascians is a major pathogen of tobacco plants. R. equi, one of the most important foal pathogens, is endemic on many stud farms around the world.
Gram-positive
Gram-positive bacteria are those that are stained dark blue or violet by Gram staining. This is in contrast to Gram-negative bacteria, which cannot retain the crystal violet stain, instead taking up the counterstain and appearing red or pink...
bacteria closely related to Mycobacteria and Corynebacteria. While a few species are pathogenic, most are benign and have been found to thrive in a broad range of environments, including soil, water, and eukaryotic cells. Fully sequenced in October 2006, the genome is known to be 9.7 megabasepairs long and 67% G/C.
Strains of Rhodococcus are applicably important owing to their ability to catabolize a wide range of compounds and produce bioactive steroids, acrylamide
Acrylamide
Acrylamide is a chemical compound with the chemical formula C3H5NO. Its IUPAC name is prop-2-enamide. It is a white odourless crystalline solid, soluble in water, ethanol, ether, and chloroform. Acrylamide is incompatible with acids, bases, oxidizing agents, iron, and iron salts...
, and acrylic acid
Acrylic acid
Acrylic acid is an organic compound with the formula CH2=CHCO2H. It is the simplest unsaturated carboxylic acid, consisting of a vinyl group connected directly to a carboxylic acid terminus. This colorless liquid has a characteristic acrid or tart smell. It is miscible with water, alcohols,...
, and their involvement in fossil fuel biodesulfurization. This genetic and catabolic diversity is not only due to the large bacterial chromosome, but also to the presence of three large linear plasmids. Rhodococcus is also an experimentally advantageous system owing to a relatively fast growth rate and simple developmental cycle. However, as it stands now, Rhodococcus is not well characterized.
Another important application of Rhodococcus comes from bioconversion, using biological systems to convert cheap starting material into more valuable compounds. This use of Rhodococcus is borne out of its ability to metabolize harmful environmental pollutants, such as toluene
Toluene
Toluene, formerly known as toluol, is a clear, water-insoluble liquid with the typical smell of paint thinners. It is a mono-substituted benzene derivative, i.e., one in which a single hydrogen atom from the benzene molecule has been replaced by a univalent group, in this case CH3.It is an aromatic...
, naphthalene
Naphthalene
Naphthalene is an organic compound with formula . It is a white crystalline solid with a characteristic odor that is detectable at concentrations as low as 0.08 ppm by mass. As an aromatic hydrocarbon, naphthalene's structure consists of a fused pair of benzene rings...
, herbicides, and PCBs. Rhodococci typically metabolize aromatic substrates by first oxygenating the aromatic ring to form a diol (two alcohol groups). Then, the ring is cleaved with intra/extradiol mechanisms, opening the ring and exposing the substrate to further metabolism. Since the chemistry here is very stereospecific, the diols are created with predictable chirality. While controlling the chirality of chemical reaction presents a significant challenge for synthetic chemists, biological processes can be used instead to faithfully produce chiral molecules in cases where direct chemical synthesis is infeasible or inefficient. An example of this is the use of Rhodococcus to produce indene
Indene
Indene is a flammable polycyclic hydrocarbon with chemical formula C9H8. It is composed of a benzene ring fused with a cyclopentene ring. This aromatic liquid is colorless although samples often are pale yellow...
, a precursor to the AIDS
AIDS
Acquired immune deficiency syndrome or acquired immunodeficiency syndrome is a disease of the human immune system caused by the human immunodeficiency virus...
drug Crixivan(TM), a protease inhibitor, and containing two of the five chiral centers needed in the complex.
Biodegradation of organic pollutants
The burgeoning amount of bacterial genomic data provides unparalleled opportunities for understanding the genetic and molecular bases of the microbial biodegradationMicrobial biodegradation
Interest in the microbial biodegradation of pollutants has intensified in recent years as humanity strives to find sustainable ways to clean up contaminated environments...
of organic pollutant
Pollutant
A pollutant is a waste material that pollutes air, water or soil, and is the cause of pollution.Three factors determine the severity of a pollutant: its chemical nature, its concentration and its persistence. Some pollutants are biodegradable and therefore will not persist in the environment in the...
s. Aromatic compounds are among the most recalcitrant of these pollutants, and lessons can be learned from the recent genomic studies of Rhodococcus sp. strain RHA1, one of the largest bacterial genomes completely sequenced to date. These studies have helped expand the understanding of bacterial catabolism
Catabolism
Catabolism is the set of metabolic pathways that break down molecules into smaller units and release energy. In catabolism, large molecules such as polysaccharides, lipids, nucleic acids and proteins are broken down into smaller units such as monosaccharides, fatty acids, nucleotides, and amino...
, noncatabolic physiological adaptation to organic compound
Organic compound
An organic compound is any member of a large class of gaseous, liquid, or solid chemical compounds whose molecules contain carbon. For historical reasons discussed below, a few types of carbon-containing compounds such as carbides, carbonates, simple oxides of carbon, and cyanides, as well as the...
s, and the evolution of large bacterial genome
Genome
In modern molecular biology and genetics, the genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA. The genome includes both the genes and the non-coding sequences of the DNA/RNA....
s. A large number of "peripheral aromatic" pathways funnel a range of natural and xenobiotic
Xenobiotic
A xenobiotic is a chemical which is found in an organism but which is not normally produced or expected to be present in it. It can also cover substances which are present in much higher concentrations than are usual...
compounds into a restricted number of "central aromatic" pathways. Some pathways are more widespread than initially thought. The Box and Paa pathways illustrate the prevalence of nonoxygenolytic ring-cleavage strategies in aerobic aromatic degradation processes. Functional genomic studies have been useful in establishing that even organisms harboring high numbers of homologous enzymes apparently contain few examples of true redundancy. For example, the multiplicity of ring-cleaving dioxygenases in certain rhodococcal isolates may be attributed to the cryptic aromatic catabolism of different terpenoids and steroids. The large gene repertoires of pollutant degraders such as Rhodococcus RHA1 have evolved principally through more ancient processes. Rhodococcus sp. strain Q1, isolated from soil and paper mill sludge, is able to degrade quinoline
Quinoline
Quinoline is a heterocyclic aromatic organic compound. It has the formula C9H7N and is a colourless hygroscopic liquid with a strong odour. Aged samples, if exposed to light, become yellow and later brown...
, various pyridine
Pyridine
Pyridine is a basic heterocyclic organic compound with the chemical formula C5H5N. It is structurally related to benzene, with one C-H group replaced by a nitrogen atom...
derivatives, catechol, benzoate, and protocatechuic acid.
Pathogenic Rhodococcus
The genus Rhodococcus has two pathogenic species: R. fasciansRhodococcus fascians
Rhodococcus fascians is a Gram positive bacterial phytopathogen that causes leafy gall disease. R. fascians is the only phytopathogenic member of the Rhodococcus genus; its host range includes both dicotyledonous and monocotyledonous hosts...
and R. equi
Rhodococcus equi
Rhodococcus equi is a Gram-positive coccobacillus bacterium. The organism is commonly found in dry and dusty soil and can be important for diseases of domesticated animals . The frequency of infection can reach near 60 percent. R. equi is an important pathogen causing pneumonia in foals. Since...
. The former, a plant pathogen, causes leafy gall disease in both angiosperm and gymnosperm
Gymnosperm
The gymnosperms are a group of seed-bearing plants that includes conifers, cycads, Ginkgo, and Gnetales. The term "gymnosperm" comes from the Greek word gymnospermos , meaning "naked seeds", after the unenclosed condition of their seeds...
plants. R. equi is the causitative agent of foal pneumonia (rattles) and mainly infects foals up to three months in age. However, it has a wide host range, sporadically infecting pigs, cattle and (immunocompromised) humans, in particular AIDS patients and those undergoing immunosuppressive therapy. Interestingly, both pathogens rely on a conjugative virulence plasmid to cause disease. In case of R. fascians, this is a linear plasmid, whereas R. equi harbors a circular plasmid. Both pathogens are economically significant. R. fascians is a major pathogen of tobacco plants. R. equi, one of the most important foal pathogens, is endemic on many stud farms around the world.
Species
- Rhodococcus aurantiacus (ex Tsukamura and Mizuno, 1971) Tsukamura and Yano, 1985, nom. rev.
- Rhodococcus baikonurensis Li, et al., 2004
- Rhodococcus boritolerans
- Rhodococcus equiRhodococcus equiRhodococcus equi is a Gram-positive coccobacillus bacterium. The organism is commonly found in dry and dusty soil and can be important for diseases of domesticated animals . The frequency of infection can reach near 60 percent. R. equi is an important pathogen causing pneumonia in foals. Since...
(Magnusson, 1923) Goodfellow and Alderson, 1977; important animal pathogen, in particular of horses and to a lesser extent pigs, cattle and goats, as well as immunosuppressed humans (e.g., AIDSAIDSAcquired immune deficiency syndrome or acquired immunodeficiency syndrome is a disease of the human immune system caused by the human immunodeficiency virus...
-patients) - Rhodococcus coprophilus Rowbotham and Cross, 1979
- Rhodococcus corynebacterioides (Serrano, et al., 1972) Yassin and SchaalBarbara A. SchaalBarbara Anna Schaal American scientist, evolutionary biologist, is a professor at Washington University in St. Louis and vice president of the National Academy of Sciences. She is the first woman to be elected vice president of the Academy...
, 2005 (synonym: Nocardia corynebacterioides (Serrano et al. 1972) - Rhodococcus erythropolis (Gray and Thornton, 1928) Goodfellow and Alderson, 1979
- Rhodococcus fasciansRhodococcus fasciansRhodococcus fascians is a Gram positive bacterial phytopathogen that causes leafy gall disease. R. fascians is the only phytopathogenic member of the Rhodococcus genus; its host range includes both dicotyledonous and monocotyledonous hosts...
(Tilford 1936) Goodfellow 1984 (synonym: Rhodococcus luteus (ex Söhngen 1913) Nesterenko et al. 1982) - Rhodococcus globerulus Goodfellow, et al., 1985
- Rhodococcus gordoniae Jones, et al., 2004
- Rhodococcus jostii Takeuchi, et al., 2002. Identified as producing a ligninLigninLignin or lignen is a complex chemical compound most commonly derived from wood, and an integral part of the secondary cell walls of plants and some algae. The term was introduced in 1819 by de Candolle and is derived from the Latin word lignum, meaning wood...
digesting enzyme, the first isolated from a bacterium rather than a fungus. - Rhodococcus koreensis Yoon, et al., 2000
- Rhodococcus kroppenstedtii Mayilraj, et al., 2006
- Rhodococcus maanshanensis Zhang, et al., 2002
- Rhodococcus marinonascens Helmke and Weyland, 1984
- Rhodococcus opacus Klatte, et al., 1995
- Rhodococcus percolatus Briglia, et al., 1996
- Rhodococcus phenolicus Rehfuss and Urban, 2006
- Rhodococcus polyvorum
- Rhodococcus pyridinivorans Yoon, et al., 2000
- Rhodococcus rhodochrous (Zopf 1891) Tsukamura, 1974
- Rhodococcus rhodnii Goodfellow and Alderson, 1979 (synonym: Nocardia rhodnii)
- Rhodococcus ruber (Kruse 1896) Goodfellow and Alderson, 1977 (synonym: Streptothrix rubra Kruse, 1896)
- Rhodococcus sp. RHA1
- Rhodococcus triatomae Yassin, 2005
- Rhodococcus tukisamuensis Matsuyama, et al., 2003
- Rhodococcus wratislaviensis (Goodfellow et al. 1995) Goodfellow, et al., 2002 (synonym: Tsukamurella wratislaviensis Goodfellow, et al., 1995)
- Rhodococcus yunnanensis Zhang, et al., 2005
- Rhodococcus zopfii Stoecker, et al., 1994
External links
- For species and synonyms see here: National Center for Biotechnology Information (NCBI)